Highly efficient suppressor-dependent protein expression in plants with a viral vector

ABSTRACT

A series of viral vectors derived from foxtail mosaic virus, sunn hemp mosaic virus and white clover mosaic virus sequences, and which are capable of expressing heterologous proteins in plants, including the tobacco,  Nicotiana benthamiana , and cowpea, bean, and other legumes with the properties of unusually limited expression in the absence of gene silencing suppressors and high level expression in their presence. In a preferred embodiment, these viral vectors may be introduced via agroinoculation, and expression of the heterologous gene may be inducible with little or no leakiness in the absence of induction.

This application claims priority to U.S. Provisional Patent Application Ser. No. 61/155,810, filed on Feb. 26, 2009, entitled HIGHLY EFFICIENT SUPPRESSOR-DEPENDENT PROTEIN EXPRESSION IN PLANTS WITH A VIRAL VECTOR, the entire content of which is hereby incorporated by reference.

FIELD OF THE INVENTION

The present invention relates to a viral vector system, and more specifically to an inducible viral vector system for expressing heterologous genes with low risk of detrimental effect of either the viral vector or of toxic protein genes carried by the vector.

BACKGROUND

Plant expression systems have been developed as a production platform for therapeutic proteins in the past two decades. Plants have some advantages over other expression systems, such as mammalian cell culture and bacterial fermentation. The application of plant systems means a lower cost of production and large-volume production, and cultivation is much less expensive and easier without sterile conditions of cell culture. Like mammalian systems, plant expression systems have the advantage of being able to produce active forms of complex proteins with post-translational modifications, such as glycosylation, which are necessary for human therapeutic proteins for correct function in vivo. Plant systems are also free of human pathogens potentially associated with mammalian cell cultures.

Although much work has been done with transgenic plants, their creation is time-consuming and labor-intensive. Plant viral vectors have emerged as the most efficient approach to achieving more rapid and higher-level expression of recombinant proteins, although protein expression is transient. Viral vectors systems take advantage of high levels of replication and maximum levels of foreign gene expression in a short time period from an engineered viral genome, with results within a week or two post-inoculation. A number of different plant viruses have been developed into protein production vectors, the most commercially useful being tobacco mosaic virus (TMV) of the Tobamovirus family and potato virus X (PVX) of the Potexvirus family.

Over the last two decades, plant virus-based expression systems have been successfully developed and utilized for high-yield production of heterologous proteins in plants. Viral vectors as transient gene expression systems provide increased speed and flexibility during early phases of experimentation. However, the potential widespread use of recombinant viruses raises concerns about possible risks to the environment. The bio-safety issues have to be considered to control the spread of the genetically engineered virus from experimental plants to susceptible wild plants. Intact viral vectors have the potential to spread and infect non-target plants, but replication-defective or movement-defective viruses avoid these problems. These deleted viral vectors can be safely used in the laboratory and, in large scale application, can be used to inoculate an entire greenhouse at once. In the field, it may be possible to achieve high expression in transgenic plants carrying an inducible virus as a transgene. In all of these cases, deleted virus vectors would be greatly preferred over full virus vectors for their lower environmental risk. However, one disadvantage of the deleted virus approach is that the vector cannot spread past the originally inoculated cells.

Several innovations have led to dramatic improvements in plant viral vectors. The early versions of these vectors cited used in vitro transcription to create infectious RNA, which is expensive and not amenable to large scale production in contrast to a more recent method named “agroinfection” (Gleba et al., 2005). Agroinfection involves syringe or vacuum infiltration of an Agrobacterium tumefaciens suspension harboring T-DNA carrying the viral genome into plant leaves, resulting in the local transformation of the infiltrated leaf with the cDNA form of the virus as a part of the T-DNA of the Ti plasmid. Agrobacterium infects each cell in the inoculated zone and inserts its T-DNA into the plant chromosome of each cell. A plant promoter placed upstream of the viral cDNA induces the transcription of viral genome in the plant nucleus and viral RNA is transported to cytoplasm for viral replication. Agroinfection results in almost 100% of the plant cells being infected transformed by Agrobacterium in the infiltrated zone. Therefore, agroinoculation also gives a preview as to how expression would look in a permanently transgenic plant. For both agroinoculation and transgenic use, systemic spread becomes an unnecessary property.

Agroinfection was developed originally for DNA plant viruses. As DNA viruses have disadvantages for foreign sequences insertion, RNA viruses were introduced into agroinfection system and developed with a number of different RNA viruses. Another development was the use of RNA silencing suppressors to increase expression. For example, a recently developed TMV vector, driven by a 35S promoter in a binary vector, was delivered via agroinfection along with an Agrobacterium culture carrying a 35S-driven p19 suppressor. This system produced 0.6-1.2 mg of recombinant protein per gram of infiltrated plant tissue, which is 10-25 times higher than the 35S promoter driven transient expression systems (Lindbo, 2007a).

Agroinfection allows the replacement of the MP and/or CP genes of vector viruses with heterologous sequences in some virus species. Tobacco mosaic virus (TMV) lacking the CP gene has been used to produce large amounts of foreign proteins and agroinfection greatly increased infectivity of the TMV cDNA, since every cell in the infiltrated area contained the TMV transgene in its nucleus. In the potato virus X (PVX) replacement virus vector, both the triple gene block (TGB) and coat protein (CP) viral genes were removed, leaving only the replicase gene, and were replaced with GFP. The expression levels of GFP from this vector were about 2.5-fold higher than that of full-length PVX vector with the GFP encoding sequence between the triple gene block and the CP genes. Removal of the movement proteins prevents systemic movement of TMV and PVX in above examples and inhibits the spread of the genetically modified virus, which is positive from the biosafety point of view.

Agrobacterium infiltration-mediated transient expression can be greatly enhanced by suppression of gene silencing. An RNA silencing suppressor (such as P19 encoded by tomato bushy stunt virus or HcPro expressed by potato virus A) is co-inoculated in a separate strain of Agrobacterium along with the Agrobacterium carrying the viral cDNA. Using this approach, highly efficient production of GFP from a TMV-based vector was achieved with up to 100-fold increase of the overexpression level (Lindbo, 2007a). As well, potexvirus expression was greatly increased (Komorova et al., 2006). Both of these viral vectors expressed GFP efficiently in the absence of GFP; however, the addition of GFP greatly increased this efficiency.

Foxtail Mosaic Virus (FoMV)

Foxtail mosaic virus (FoMV) is a member of the genus Potexvirus. Potexvirus is a large group of flexous and filamentous plant viruses with a single-stranded, positive-sense genomic RNA, with a cap structure at the 5′ terminus and a poly-(A) tail at the 3′ terminus. The FoMV genome structure resembles that of PVX, the type species of the genus Potexvirus, and the gene functions are presumed to be similar as well. The genome of FoMV contains five open reading frames (ORFs), and two subgenomic promoters directing transcription of subgenomic RNAs 1 and 2 (sgRNA1 and sgRNA2). The genomic RNA allows the expression of ORF1 encoding for the RNA-dependent RNA polymerase (RdRP) with methyltransferase, helicase, and polymerase motifs. ORF2, 3 and 4 code for the triple gene block (TGB) proteins TGB1, TGB2 and TGB3, which are required for virus cell-to-cell movement. ORF2 codes for a multifunctional protein that has RNA helicase activity, promotes translation of viral RNAs, increases plasmodesmal size exclusion limits, and acts as a suppressor of RNA-mediated post-transcriptional gene silencing (PTGS). ORF5 encodes the coat protein, which is required for viral encapsidation and long distance movement. FoMV has a broad host range, infecting 56 species of the Gramineae and at least 35 dicot species. The sequence of FoMV genomic RNA was first published in 1991. Infectious full-length clones were constructed based on the same FoMV isolate and some corrections to the published sequence were noted. The significant difference between the gene organizations of FoMV and PVX is the presence of ORF 5A upstream of the CP gene in FoMV. ORF 5A initiates 143 nts upstream of the CP and extends the reading frame of CP gene. The 5A protein was produced in vivo, but it was not required for either replication or productive infection of plants. Recently, the revised full-length sequence of Foxtail mosaic virus clone was published in 2008 (Bruun-Rasmussen et al.), and reveals a triple gene block structure similar to potato virus.

Foundational potexvirus vector work was done first not with FoMV but with PVX, the type species of the genus Potexvirus. PVX was engineered to express reporter proteins such as GFP and GUS, which were cloned just upstream of the CP gene and expressed from a duplicated copy of the coat protein (CP) subgenomic promoter. The reporter protein is translated from a sgRNA separate from the other viral proteins. Because PVX has a linear helical capsid, rather than an icoshedral capsid, the longer than wild type recombinant viral genome can still be encapsidated into infectious virus particles. However, GUS encoding sequence was deleted, because of recombination between the homologous sequences of the duplicated subgenomic promoters (81 nt).

The potexvirus replicase is the only protein translated directly from the full-length genomic RNA, but other viral proteins are translated from 3′ coterminal subgenomic RNAs (sgRNAs). The two sgRNAs of approximately 2.1 and 0.9 kb in length have their 5′ termini upstream of the TGB and CP genes, respectively. The integrity of subgenomic promoter is very important for the accumulation of subgenomic RNA and target protein. However, the boundaries of sgRNA promoters have not been delineated for FoMV.

Therefore, what is needed in either a greenhouse or field setting is a viral vector which expresses protein at a very high level and yet is intrinsically crippled, greatly facilitating decontamination and lowering environmental risk. As well, an inducible version of such a viral vector which expresses an exogenous gene at high levels in the presence of a silencing suppressor, and expresses the exogenous gene at negligible levels in the absence of a silencing suppressor would further lower environmental risk and would facilitate the manipulation of plant material transformed with such a viral vector, such as in the production of transgenic plants.

SUMMARY

In a preferred embodiment, the present invention comprises a viral vector derived from Foxtail mosaic potexvirus, wherein the triple gene block and coat protein genes have been removed, specifically with partial removal of the TGB1 and CP open reading frames, and wherein expression is driven by a CaMV 35S promoter. The invention further comprises a method of expressing a gene in a plant comprising inserting the gene into the viral vector and delivering the viral vector to a plant using agroinoculation of Agrobacterium tumefaciens. In a preferred embodiment, the plant may be Nicotiana benthamiana. In a further preferred embodiment, the method may include the step of co-inoculating with silencing suppressor genes carried in a separate agrobacterial strain.

In a further preferred embodiment, the present invention comprises a viral vector derived from Sunn hemp mosaic virus (SHMV), wherein the coat protein open reading frame has been partially removed, and wherein expression is by a CaMV 35S promoter. The endogenous coat protein may be replaced by the coat protein open reading frame and subgenomic promoter from another tobamovirus. The invention further comprises a method of expressing a gene in a plant comprising the steps of inserting the gene into the viral vector and delivering the viral vector to a plant using agroinoculation of Agrobacterium tumefaciens. In a preferred embodiment, the plant may be Nicotiana benthamiana. In a further preferred embodiment, the method may include the step of co-inoculating with silencing suppressor genes carried in a separate agrobacterial strain. The silencing suppressor genes may be RNA silencing suppressor p19 or HcPro.

In a further preferred embodiment, the present invention comprises a viral vector derived from White clover mosaic potexvirus, wherein the triple gene block and coat protein genes have been removed, specifically with partial removal of the TGB1 and CP open reading frames, and wherein expression is driven by a CaMV 35S promoter. The invention further comprises a method of expressing a gene in a plant comprising inserting the gene into the viral vector and delivering the viral vector to a plant using agroinoculation of Agrobacterium tumefaciens. In a preferred embodiment, the plant may be Nicotiana benthamiana. In a further preferred embodiment, the method may include the step of co-inoculating with silencing suppressor genes carried in a separate agrobacterial strain.

In a further preferred embodiment, the invention comprises an inducible viral vector system derived from the Foxtail mosaic virus, carried on one binary vector, wherein the triple gene block and coat protein genes have been removed, specifically with partial removal of the TGB1 and CP open reading frames, and wherein viral vector transcription is driven by a constitutive promoter, such as the CaMV 35S promoter, or an inducible promoter, such as an estradiol-inducible promoter, and wherein a second binary vector is included, comprising an inducible promoter, such as an estradiol-inducible promoter, which allows for expression of a silencing suppressor, such as p19, and may also include a gene constitutively expressing the XVE transcription factor. This method may further include the steps of co-agroinoculating the two Agrobacterium cultures into a plant, preferably Nicotiana benthamiana, and delivering estradiol to the plant.

It is herein disclosed that these vectors would serve as an enabling technology for the development of transgenic plants which would produce foreign proteins upon induction. Since the process of agroinoculation creates a zone of leaf tissue comprising transgenic plant cells while retaining the mature leaf morphology, and since this transgenic leaf tissue was capable of expressing large quantities of foreign protein, and since this transgenic leaf tissue was capable of being induced by estradiol, it would be expected that transgenic whole plants would express the quantities of protein seen in this study and would be capable of expressing this in an inducible fashion. Furthermore, since there was little or no leakiness of expression of GFP or toxic glycanases by these viral vector in the absence of p19, we disclosed that it should be possible to create such transgenic plants carrying these vectors, driven by either constitutive or inducible promoters, because any detrimental effect of either the viral vector or of toxic protein genes carried by the vector would be mitigated by the very low level of leakiness.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIG. 1 shows a schematic diagram of the T-DNA regions of binary plasmid used in this study (A) and the genomic organization of FoMV-based replicon (B). (A)—Cauliflower mosaic virus (CaMV) 35S promoter driven versions of Foxtail mosaic virus (FoMV) vector cDNAs or FECT as viral vector to express GFP, GUS and antibody LC, HC and 35S driven versions of GFP, p19 were constructed. All plasmids were based on the binary vector pCB301 backbone. Open boxes represent open reading frames; black stars: left border and right border of T-DNA; block arrows: CaMV duplicated 35S promoter; black boxes: CaMV 3′ terminator sequence; gray arrows, subgenomic promoters; white arrow: nos promoter (Pnos); white box: nos terminator (Tnos); dark grey boxes: Tobacco etch virus 5′ non-translated leader sequence (L); RB: T-DNA right border sequences; LB: T-DNA left border sequences; TGB: triple gene block; CP, coat protein; LC, antibody light chain; HC, antibody heavy chain. (B)—All TGB and CP deletion mutants have the root “FECT” (Foxtail Elimination of CP and TGB). In the start codon of 5′TGB, ATG were mutated to ATC, shown as underlined. Restriction sites PacI and AvrII were introduced at the flank of GFP ORF as cloning sites for other foreign inserts. The numbering indicates the number of nucleotides from the TGB ORF presented as upstream of the GFP ORF. For example, FECT40 remains the 5′ end 40 nts of FoMV TGB to reserve the subgenomic promoter to drive the expression of GFP;

FIG. 2 shows schematic diagram of the T-DNA regions of binary plasmid used in this study (A) and the genomic organization of SHMV-based replicon (B). (A). 35S promoter-driven versions of Sunn hemp mosaic virus (SHMV) vector cDNAs and 35S driven GUS, p19 and HcPro were constructed. All plasmids were based on the binary vector pCB301 backbone. Open boxes represent open reading frames; black stars: left border and right border of T-DNA; block arrows: CaMV duplicated 35S promoter; light grey box: ribozyme; black boxes: CaMV 3′ terminator sequence; gray arrows, subgenomic promoters; dark grey boxes: Tobacco etch virus 5′ non-translated leader sequence (L); RB: T-DNA right border sequences; LB: T-DNA left border sequences. SHMV transcripts are processed by a ribozyme to generate authentic TMV 3′ ends. (B). All CP deletion mutants have the root “SHEC” (Sunn Hemp Elimination of CP). In the start codon of 5′CP, two ATGs were mutated to ACGs, shown as underlined. Restriction sites PacI and BssHII were introduced at the flank of GFP ORF as cloning sites for other foreign inserts. The numbering in each construct name indicates the number of nucleotides of CP ORF retained to increase GFP expression. For example, SHEC58 retains the 5′ end 58 nts of SHMV CP to lengthen the subgenomic promoter to drive the expression of GFP, and SHEC/GFP-40 CP 3′ retains the 3′ end 40 nts of SHMV CP to increase protein expression;

FIG. 3 shows diagrams of the key estradiol-inducible binary vectors agroinoculated in this study. JBest was constructed here to be the parent of TBest and FBest. pER8 (Zuo et al., 2000) was the parent of pER8/p19. LB, RB: left and right T-DNA borders; Pnos, Tnos: promoter and transcriptional terminator from nopaline synthase gene; LexAO: regulatory element that binds to estradiol-inducible XVE transcription factor; 35S core: combined with LexAO as inducible promoter; replicase: viral methylase, helicase and RdRp; MP, viral movement protein, sgp1: subgenomic promoter driving gene of interest (GOI); sgp2: subgenomic promoter driving viral coat protein (CP) gene; 35Sterm: transcription terminator; G10-90: synthetic promoter; XVE: estradiol-inducible transcription activator; E9term: pea rbcS E9 terminator; hygR: hygromycin resistance; p19: silencing suppressor; 3Aterm: pea3A terminator;

FIG. 4 shows primers used in vector constructions;

FIG. 5 shows the construction of pJL22/WClMV. The white clover mosaic virus cDNA sequence was transferred from an in vitro transcription vector background to a binary vector background. The 5′ portion of the viral cDNA was transferred to the binary vector, JL22, followed by transfer of the 3′ portion. The middle section was added via native AvrII and AatII sites to create pJL22/WClMV;

FIG. 6 shows construction of the WECTatg vector from JL22WClMV. The triple gene block (TGB) and coat protein (CP) genes were removed, wholly or partially, by subcloning the 3′ viral sequence to cloning vector pNEB193 and then adding the 5′ viral sequence upstream of this. The combined structure, with the deletion in the center, was subcloned back into JL22WClMV to create WECTatg. Primer numbers as in Table 3; and

FIG. 7 shows removal of the start codon of the residual TGB1 open reading frame from WECTatg to create WECT25 and WECT40. A primer containing the sequence ATC (replacing the ATG start codon) was used to create a PCR product which was then inserted back into WECTatg to create WECT25. WECT 25 served as the template to create WECT40. Primer numbers as in Table 3.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

The present invention relates to an inducible viral vector which expresses an exogenous gene at high levels in the presence of a silencing suppressor, and expresses the gene at negligible levels in the absence of a silencing suppressor.

In this study, vectors were constructed which exhibited two advantageous properties: (1) compared to other viral vectors factors, the environmental risks are greatly lowered and (2) the expression rate of foreign proteins is among the highest achieved in plant systems to date. To achieve lowered environmental risk, the TGB and CP genes of FoMV were removed and replaced with heterologous sequences while the subgenomic promoter of one of the TGB genes was reserved to direct the transcription of the heterologous coding sequence. The FoMV expression vectors driven by the cauliflower mosaic virus (CaMV) 35S promoter were delivered as a T-DNA to plant cells by Agrobacterium tumefaciens. This viral vector is unprotected by a coat protein, was not able to infect Nicotiana benthamiana systemically, replicates very poorly, and has had its genome size reduced by 29%. On the other hand, in the presence of gene silencing suppressor, the virus-mediated expression of the reporter protein GFP was up to 1.4 ug/g fresh weight of plant leaf (40% total soluble protein).

In a preferred embodiment of the invention, these vectors would be useful in the development of transgenic plants which would produce foreign proteins upon induction. Since the process of agroinoculation creates a zone of leaf tissue comprising transgenic plant cells while retaining the mature leaf morphology, and since this transgenic leaf tissue was capable of expressing large quantities of foreign protein, and since this transgenic leaf tissue was capable of being induced by estradiol, transgenic whole plants would also express the quantities of protein described in this application and would be capable of expressing this in an inducible fashion. Furthermore, since there was little or no leakiness of expression of GFP or toxic glycanases by these viral vector in the absence of p19, transgenic plants carrying these vectors, driven by either constitutive or inducible promoters, would not experience detrimental effects of either the viral vector or of toxic protein genes carried by the vector because these effects would be mitigated by the very low level of leakiness.

Sunn Hemp Mosaic Virus (SHMV)

By far, the current emphasis in commercial and scientific use of viral vectors lies with the tobacco host Nicotiana benthamiana. Future development needs to focus on the creation of new vectors that can be used in different hosts, such as hosts amenable to oral delivery of vaccines, including cereals and legumes. Sunn Hemp Mosaic virus (SHMV) is a good candidate for such a vector, since it is closely related to the commercially robust TMV but it infect a wide range of legumes as well as N. benthamiana.

SHMV, being a member of the Tobamovirus group, is a plus-strand RNA virus with the same genomic arrangement as TMV. The 3′ 1.8 kb of sequence were determined in initial reports, while the final 4.6 kb at the 5′ end were given in a separate report, completing the sequence (Silver et al., 1996). Belonging to the tobamovirus group, SHMV is a positive strand RNA virus consisting of 6483 nucleotides. Like TMV, the SHMV genome consists of genes coding for two replicase proteins, a movement protein and a coat protein (CP). The first two open reading frames (ORF) produce two replicase proteins, a 129 kDa and an 186 kDa protein. An amber stop codon at the end of the 126 kDa replicase undergoes a translational read-through to produce the 183 kDa replicase. The movement and coat proteins are translated from 3′ coterminal subgenomic mRNAs. The movement protein is a 31 kDa protein produced early in the infection cycle, which is required for virus cell to cell movement. The coat protein is 18 kDa protein produced at high levels later in the infection cycle, and is required for virus long distance movement.

By deletion of the CP gene, a viral vector has been constructed, SHEC (Sunn Hemp Elimination of Coat protein), that is incapable of long distance movement and is unprotected by a coat protein. The coat protein subgenomic promoter was used in this vector to drive foreign genes, using three different potential promoter lengths. The use of co-agroinoculation with a silencing suppressor gene was found to be critical for successful marker gene expression. In the absence of the suppressor, the expression level was negligible, similar to the FECT vector of foxtail mosaic virus. This is in contrast to a similar CP-deletion mutant derived from tobacco mosaic virus (TMV), also a tobamovirus family member, which expressed well even in the absence of a silencing suppressor (Lindbo, 2007b). A full length vector was also created. A subgenomic promoter from a different tobamovirus was needed to drive the coat protein gene (in addition to the SHMV coat protein promoter driving the foreign gene), since recombination between identical subgenomic promoters has be shown to severely destabilize TMV vectors. This chimeric viral vector with an Alternate Coat protein (SHAC) systemically infected N. benthamiana and expressed GFP.

White Clover Mosaic Virus (WCLMV)

White clover mosaic virus (WClMV) is a member of the genus Potexvirus like foxtail mosaic virus (FoMV) mentioned previously. It contains all the basic features in its genome, replication and expression strategy, and virus particle as already described for FoMV. It is distinguished from FoMV, and is similar to SHMV, in that it has a much broader host range in Fabaceae, the legume family, which includes a wide variety of plants critical to human nutrition such as beans, peas, and cowpeas and forage crops such as clover. WClMV was chosen in this project as a base for the construction of an agroinfection viral vector because of its host range in legumes, its success as a nonagroinfection viral vector (Beck et al, 1990), and its similarity to FoMV. Because the deleted version of FoMV (FECT) demonstrated very high expression of the presence of a gene silencing suppressor and yet is nearly environmentally inert in its absence, and yet a similar potato virus X vector (Komorova et al., 2006), from the same potexvirus family, did not display this stark “on/off” capacity, it was investigated whether this effect could be duplicated in another member of the potexvirus family. Similar to the FECT construction, the TGB and CP genes of WClMV were removed and replaced with heterologous sequences while the subgenomic promoter of one of the TGB genes was reserved to direct the transcription of the heterologous coding sequence. The WClMV expression vector driven by the cauliflower mosaic virus (CaMV) 35S promoter was delivered as a T-DNA to plant cells by Agrobacterium tumefaciens via agroinfection. As with the FECT vector, high levels of GFP expression were seen in the presence of silencing suppressor while almost no expression occurred in the absence of silencing suppressor.

Inducible Viral Vectors

Inducible expression systems are desirable when a protein detrimental to the host organism is to be expressed. In plants, several inducible promoters have been used successfully, including those induced by copper, dexamethasone, ethanol, estradiol (Zuo et al., 2000), and ecdysone. Of these the estradiol and ecdysone systems report the highest expression of marker genes, with several-fold higher expression than the CaMV 35S promoter.

Since viral vectors provide much higher expression than this, there has been an impetus to produce inducible viral vectors. This concept has two potential problems, however. First, viral vectors come with some concerns regarding environmental safety, since they are capable of replication and transmission in the field. Second, there is the potential for leakiness in the uninduced plant, since a single viral replicon transcribed from the inducible viral transgene is a self-amplifying replicon which can move from cell to cell.

Four inducible viral systems have already been developed. Two consist of full-length viral vectors: a dexamethasone-inducible Brome mosaic virus (BMV) vector and an estradiol-inducible Cucumber mosaic virus (CuMV) vector (Sudarshana et al., 2006). Two others utilize a deleted virus system: an ethanol-inducible Bean yellow dwarf virus (BYDV) vector (Zhang and Mason, 2006) and an estradiol-inducible Tomato mosaic virus (ToMV) vector. The BMV and BYDV vector systems were demonstrated in transgenic whole plants, while the ToMV system used transgenic tobacco cell cultures. The CuMV vector system was demonstrated via agroinoculation.

As described herein, a highly deleted viral vector from Foxtail mosaic virus (Potexvirus family) has been created, which is a virus noteworthy in causing mild symptoms in its hosts. This FECT vector (FoMV elimination of coat protein and triple gene block) would be an excellent candidate for development into an inducible viral vector of enhanced environmental safety. FECT is capable of expressing GFP in Nicotiana benthamiana at up to 40% total soluble protein but only with co-expression of a silencing suppressor such as p19. In the absence of suppressors, FECT expresses little or no protein. FECT has 29% of its genome removed and retains only the replicase complex, the 5′ and 3′ UTRs and the TGB1 subgenomic promoter.

Described herein is an estradiol-inducible FECT vector, herein named FBest (FECT/bar estradiol-inducible). Agroinoculation was used as a model anticipating the properties that would be seen in stably transgenic plants. In agroinoculation, the cells in the infiltrated zone are made transgenic, with the genes contained within the TDNA, including the viral vector, inserted into a chromosome of the plant cell. FBest expressed GFP with fluorescence similar to the FECT vector and dependent on p19 co-expression like FECT. Furthermore, FBest can express a toxic gene product (xylanase) with total necrosis of the leaf occurring only after induction with estradiol. The several safety features of the FBest vector would be valuable for large scale agroinoculation in greenhouses or in any potential use of the vector in stably transgenic plants. In this latter case, the ability to express proteins toxic to plants would be most useful, permitting the survival of the plants during tissue culture, seed production and initial growth in the field.

I Viral Vector Derived from Foxtail Mosaic Potexvirus (FoMV)

The present invention comprises a viral vector derived from Foxtail mosaic potexvirus (FoMV), wherein the TGB2, TGB3, and most of the TGB1 and coat protein (CP) genes have been removed, and wherein expression is driven by a CaMV 35S promoter. The invention further comprises a method of expressing a gene in a plant comprising inserting the gene into the viral vector and delivering the viral vector to a plant using agroinoculation of Agrobacterium tumefaciens. In a preferred embodiment, the plant may be Nicotiana benthamiana. In a further preferred embodiment, the method may include the step of co-inoculating with silencing suppressor genes carried on the same or a separate agrobacterial strain.

In a preferred embodiment, the invention comprises a viral vector comprising a binary vector which includes a multiple cloning site, a CaMV 35S promoter at the 5′ end of the multiple cloning site, and a 35S polyA signal/transcription terminator at the 3′ end of the multiple cloning site. The binary vector may be pJL22. The viral vector further comprises a foxtail mosaic virus full length cDNA inserted into the multiple cloning site of the binary vector. The foxtail mosaic virus full length cDNA may have had the majority of the Triple Gene Block (TGB) deleted, while retaining the subgenomic promoter of subgenomic RNA I retained including approximately the first 30% or less of the TGB1 ORF, preferably the first 20% of the TGB1 ORF, most preferably approximately 6% of the TGB1 ORF comprising the first 40 by out of the 711 by in the full sequence. The foxtail mosaic virus full length cDNA may have had the majority of the coat protein (CP) removed, while retaining the final sequence of the CP ORF including approximately 30% or less of the terminal sequence of the CP ORF, preferably approximately 20% or less of the terminal sequence of the CP ORF, most preferably approximately 6% of the terminal sequence of the CP ORF comprising the final 42 by out of the 648 by sequence.

The invention further comprises the insertion of a heterologous gene into a restriction site at the 3′ end of the subgenomic promoter of subgenomic RNA1 in the foxtail mosaic virus full length cDNA within the binary vector.

In a further preferred embodiment, the invention also comprises a process for expressing a gene in a plant comprising the step of: agroinoculating the plant with the viral vector described above. In this embodiment, the plant could be Nicotiana benthamiana, cowpea, lentil, bean, switchgrass, foxtail millet, barley, wheat, oat or corn, and the gene could be a marker gene, such as glucuronidase, DsRed, GFP, a gene for a cell wall modifying agent such as cellulase, glycanase, pectinase or LTP, or an antibody fragment such as anti-langerin mAb IgG4 heavy chain or the anti-langerin mAb IgG4 light chain.

II Viral Vector Derived from Sunn Hemp Mosaic Virus (SHMV)

The present invention comprises a viral vector derived from Sunn hemp mosaic virus (SHMV), wherein at least 70% of the coat protein (CP) open reading frame has been removed, and wherein 20% or less of the initial portion and 10% or less of the final portion of the open reading frame of the coat protein has been retained, and wherein transcription of the viral vector is driven by a CaMV 35S promoter. The gene of interest is inserted between the initial and final CP ORF sequences. The start codon of the coat protein may be mutated to be nonfunctional. The endogenous coat protein may be replaced by the coat protein open reading frame from another tobamovirus. The invention further comprises a method of expressing a gene in a plant comprising the steps of inserting the gene into the viral vector and delivering the viral vector, contained in a binary vector, to a plant using agroinoculation of Agrobacterium tumefaciens. In a preferred embodiment, the plant may be Nicotiana benthamiana. In a further preferred embodiment, the method may include the step of co-inoculating with silencing suppressor genes carried in a separate agrobacterial strain. The silencing suppressor genes may be RNA silencing suppressor p19 or HcPro.

In a preferred embodiment, the invention comprises a viral vector comprising a binary vector which includes a multiple cloning site, a CaMV 355 promoter at the 5′ end of the multiple cloning site, and a 35S polyA signal/transcription terminator at the 3′ end of the multiple cloning site. The binary vector may be pJL22. The viral vector further comprises a Sunn hemp mosaic virus full length cDNA inserted into the multiple cloning site of the binary vector. The Sunn hemp mosaic virus full length cDNA may have had the majority of the coat protein (CP) deleted, while retaining approximately 30% or less of the of the initial sequence of the CP ORF, preferably approximately 20% or less of the initial sequence of the CP ORF, most preferably approximately 15% of the CP ORF comprising the initial 74 by out of the 495 by sequence. The Sunn hemp mosaic virus full length cDNA may have had the majority of the coat protein (CP) deleted, while retaining the subgenomic promoter of CP subgenomic RNA will be retained, comprising approximately 20% or less of the of the final sequence of the CP ORF, preferably approximately 10% or less of the final sequence of the CP ORF, most preferably approximately 0% to 5% of the CP ORF comprising the final 0 by to 25 by out of the 495 by sequence.

The invention further comprises the insertion of a heterologous gene into a restriction site at the 3′ end of the subgenomic promoter of subgenomic RNA1 in the Sunn-hemp mosaic virus full length cDNA within the binary vector.

In a further preferred embodiment, the invention also comprises a process for expressing a gene in a plant comprising the step of agroinoculating the plant with the viral vector described above. In this embodiment, the plant could be Nicotiana benthamiana, pinto bean, or cowpea, and the gene may be GFP or GUS.

III Inducible Viral Vector System

The present invention comprises an inducible viral vector system derived from the Foxtail mosaic virus (SEQ ID NO: 7). The Foxtail mosaic virus comprises a 5′ untranslated region (UTR) (SEQ ID NO:1), a replicase (SEQ ID NO:2), a TGB1 open reading frame (SEQ ID NO: 3), TGB2 and TGB3 genes (SEQ ID NO: 4), a CP gene (SEQ ID NO:5), and a 3′ UTR (SEQ ID NO: 6). In the present invention, the triple gene block (TGB) and coat protein (CP) genes have been removed, leaving approximately the first 30% or less of the TGB1 ORF, preferably the first 20% or less of the TGB1 ORF, most preferably the first 6% or less of the TGB1 ORF, and also retaining approximately 30% of the final sequence of the CP ORF, preferably approximately 20% of the final sequence of the CP ORF, and most preferably 6% of the final sequence of the CP ORF, and wherein transcription of the viral vector is driven by a CaMV 35S promoter or by an inducible promoter, preferably a promoter regulated by the estradiol-inducible XVE transcription activator. The invention further comprises a method of expressing a gene in a plant comprising the steps of inserting the gene into the viral vector and delivering the viral vector to a plant using agroinoculation of Agrobacterium tumefaciens, and delivering a pER8 plasmid containing a constitutively expressed XVE transcription factor and a p19 ORF driven by another XVE-targeted promoter via a second Agrobacterium line. This method may further include the steps of co-agroinoculating the Agrobacterium cultures into a plant, preferably Nicotiana benthamiana, and delivering estradiol to the plant.

IV Creating Whole Transgenic Plants Containing Vectors

The invention further comprises creating transgenic whole plants using the vectors described herein. A selectable marker gene (such as the bar gene in the FBest vector of this application) would be contained within the T-DNA segment harboring the viral vector on one binary plasmid and this would need to be maintained by an Agrobacterium culture containing a disarmed Ti plasmid. A second binary plasmid (such as pER8/p19) containing a constitutively expressed inducible transcription factor (such as XVE), an inducibly expressed gene silencing protein (such as p19), and a second selectable marker gene would be maintained in a second Agrobacterium culture. The two sterile Agrobacterium cultures would then be centrifuged and resuspended sterilely in buffer containing magnesium and acetosyringone to stimulate the infection process. The two bacterial suspensions would be mixed and surface-sterilized leaf pieces would be dipped in these suspensions then transferred to a nutrient agar plate containing no antibiotics for 1-2 days to allow for agroinoculation to occur. The inoculated leaf pieces would then be transferred to agar medium containing the two appropriate antibiotics or herbicides for selection of transformants, an additional antibiotic to eliminate residual Agrobacterium (such as carbenicillin) and hormones appropriate for the production of shoots. After the appearance of shoots, the shoots would be excised and transferred to agar medium containing the double transformant-selective antibiotics and hormones appropriate for the production of roots. Upon the production of roots, rooted shoots would be transferred to soil medium and gradually acclimated to greenhouse conditions. Such whole transgenic plants would be screened for the presence of viral sequence, p19 and XVE (e.g., via PCR), screened for functionality by induction with inducer and detection of the payload gene product carried by the viral vector. Lines with good expression would be used to generate seed, and seed carrying both constructs could be selected by sprouting the seed on agar plates containing both antibiotics. Examples of the production of transgenic whole plants expressing a viral vector can be found in the literature (Zhang and Mason, 2006)

Example 1 Plants

Panicum virgatum cv. Blackwell (switchgrass), Setaria viridis (foxtail grass), Hordeum vulgare (barley), Triticum aestivum (wheat), Avena sativa (oat), Zea mays (corn), Phaseolus vulgaris (bean), Lens culinaris (lentil), Vigna unguiculata (cowpea) and Medicago trunculata (a legume model system plant) plants were germinated from seed and grown in growth pots with exposure to 24 h per day with illumination from plant-adapted spectrum fluorescent bulbs at temperatures ranging from 22 to 24° C. Plants 2-3 weeks from seed, with fully expanded leaves, were used for agroinfiltration and inoculation experiments. Nicotiana benthamiana was grown from seed and then transplanted and grown under 400W metal halide lamps to 10-15 cm before inoculation.

Plasmid Constructs

All FoMV viral cDNA constructs used in this study are derivatives of a wild-type FoMV cDNA clone that was a gift from Nancy Robertson of the USDA (Robertson et al., 2000) and were constructed with standard recombinant DNA techniques. The binary vector, pJL22, provided by John Lindbo (Lindbo, 2007a), has the mini binary plasmid, pCB301, as backbone. JL22 contains multiple cloning sites (MCS) flanked by a 35S promoter and 35S polyA signal/transcription terminator.

1. pFoMV/JL22

FoMV full length viral cDNA was inserted into MCS of pJL22 using standard cloning procedures. FoMV full length viral cDNA obtained from Robertson already had 70 adenosine residues at its terminus, followed by a Xba I site. The 5′ end of FoMV was amplified by PCR with primers FoMV5′ termUP and FoMV756NotDown and cut with NotI. The 5′ end of FoMV was cloned into JL22 backbone cut with StuI and NotI to create JL22/FoMV5′. The 3′ end of FoMV was prepared by restriction digest with PmlI and XbaI and then cloned into the JL22/FoMV5′ backbone cut with PmlI and XbaI. JL22 contains CaMV 3′ polyA signal to generate authentic FoMV 3′ polyA ends. This full viral cassette including promoter, terminator is flanked with Left Border and Right Border of T-DNA (FIG. 1).

2. pFECT0, pFECT22 and pFECT40

Primers were designed to delete the TGB and CP genes and keep the subgenomic promoter of sgRNA1 and 3′-end of the CP gene in the FoMV genome. The start codon AUG of TGB1 was mutated to AUC. To ensure that the sgRNA1 promoter of FoMV constructs to drive GFP had been fully cloned, primers were created to include the first 0, 22 and 40 bases of ORF of TGB1 to create pFECT0, pFECT22 and pFECT40, respectively. Restriction enzyme sites PacI and AvrII sites were placed right after the reserved subgenomic promoter of TGB1. Primer FoMV+0sgpDown (SEQ ID NO:97) added both AvrII and PacI sites at 3′ end of subgenomic promoter TGB1 and primer FoMVUp (SEQ ID NO:96) was upsteam of unique BamHI site. With these two primers, the amplified PCR fragment was digested with BamHI and AvrII and cloned into vector backbone cut with same restriction endonucleases to create pFECT0. Subsequently, two primers FoMV+22sgp (SEQ ID NO:98) and FoMV+40sgp (SEQ ID NO:99) were pared with FoMVUP to generate two PCR fragments including 22 and 40 bases of TGB1 ORF respectively. Then, pFECT0 cut with BamHI and PacI was used as vector backbone to clone two DNA fragments to create pFECT22 and pFECT40. AvrII enzyme site presented at the 3′ end of CP gene originally and was utilized as a restriction cloning site to insert foreign gene for expression. The 3′ terminal part of CP FoMV gene between AvrII and 3′-UTR was reserved in the viral vector, because it is crucial for the efficient expression of viral vector. Deletion of this region dramatically reduced the viral replication and accumulation (Komarova et al., 2006).

The FECT40 vector (SEQ ID NO:34) comprises a 5′ UTR (SEQ ID NO:21), a replicase (SEQ ID NO:22), 40 by of the TGB1 ORF plus Pac I and Avr II cloning sites (SEQ ID NO: 23), the last 42 by of the CP ORF (SEQ ID NO: 24), a 3′ UTR (SEQ ID NO:25), a poly(A) tract (SEQ ID NO:26), a 35S terminator (SEQ ID NO:27), miscellaneous sequence (SEQ ID NO:28), a T-DNA right border (SEQ ID NO:29), a JL22 sequence (SEQ ID NO: 30), a T-DNA left border (SEQ ID NO:31), miscellaneous sequence 2 (SEQ ID NO: 32), and a 35S promoter (SEQ ID NO:33).

TABLE 1 Primers used for plasmid construction in FoMV study. SEQ ID Oligonucleotide Plasmid NO Primer sequence (5′-3′) Purpose pFoMV/JL22 92 FoMV 5′ term UP P-GAAAACTCTTCCGA The 5′ end of FoMV was amplified by (pFoMV nt. 1-21) AACCGAA PCR with primers FoMV5′termUP and 93 FoMV756 NotI DOWN TTTTTTGCGGCCGCTTAGCCA FoMV756NotDown and cut with PmlI. (pFoMV nt. 737-757) GTTTAGGTCCTTA The 3′ end of FoMV was digested with PmlI and XbaI. Both 5′ and 3′ end fragments of FoMV were cloned into the JL22 backbone cut with StuI and XbaI. pFECT0 96 FoMV Up GTGGGCATGTGCAGATGAGG To create ΔTGB/ΔCP mutants, PacI and pFECT22 (pFoMV nt AvrII cloning sites were introduced by pFECT40 3044-3063) PCR amplified with two primers 97 FoMV + 0sgp Down AACCTACCTAGGACTTTAATT FoMVUp and FoMV + Osgp Down). (pFoMV nts.4114- AATGTTATTTAATTCGTCAGT PCR with mutated start codon of TGB 4131) G was cut with BamHI and AvrII and 98 FoMV + 22sgp Down GCTTTTAATTAAGTTCAACTA cloned into pFoMV vector backbone to (pFoMV nts.4124- TTTCACTATCGATTGTTATT create pFECT0. Other two downstream 4153) primers (with PacI site) were used to 99 FoMV + 40sgp Down GTCTTTAATTAACCAAGCTTT save 22 nts and 40 nts 5′ end of TGB (pFoMV nts.4150- GTTAGTCGTTC DNA sequence. PCR fragments were 4169) cloned in pFECTO vector backbone cut with BamHI and PacI to generate pFECT22 and pFECT40. pFECT0/GFP 100 PacGFPUp TTGTCATTAATTAAGCTAGCA To clone the GFP ORF into the pFECT pFECT22/GFP AAGGAGAAGAAC vector. Primer PacGFPUp adds a PacI pFECT40/GFP 101 GFPAvrDown TTTACTCCTAGGTTATTTGTA site (underline) at the 5′ end, and GAGCTCATCCA primer GFPAvrDown adds an AvrII site (underline) to the 3′ end. pFECT40/DsRed 102 PacDsRedUP GGATGGTTAATTAAATGGCCT DsRed and anti-Langerin antibody light pFECT40/LC CCTCCGAGAACG chain and heavy chain genes were PCR pFECT40/HC 103 AvrDsRedDN TTTACTCCTAGGCTACAGGAA mutagenized to be flanked with PacI and CAGGTGGTG AvrII restriction sites on 5′- and 3′- 104 PacLangLCUP GGATGGTTAATTAAATGAAGT ends, correspondingly. The three gene TGCCTGTTAGGCT fragments were cloned into the 105 AvrLangLCDN AATACTCCTAGGCTAACACTC PacI/AvrII sites of the pFECT40 to TCCCCTGTTG generate pFECT40/DsRed, 106 PacLangHCUP ATATGGTTAATTAAATGGAAT pFECT40/LC and pFECT40/HC GGAGGATC TTTCT constructs. 107 AvrLangHCDN TTTACTCCTAGGTCAGCTAGC TTTACCCAGAG pFECT40/GFP/ 108 ApaI Pnos UP ATATGAGGGCCCAACTGAAG To add PnosTnos in pFECT40, and PnosTnos GCGGGAAACGACAATC create BsiWI and SpeI in between Pnos 109 PnosBsiWI- GACCACTTTATGGAGGTTCGT and Tnos. Inner primers PnosBsi- overlapDN ACGTCTAGGGGATCCGGTGC overlapDN and TnosSpe-overlapUP AG have overlap sequence and BsiWI and 110 TnosSpeI- AACCTCCATAAAGTGGTCACT SpeI sites. Two inner primers pair with overlapUP AGTATCGTTCAAACATITGGC outer primers ApaPnosUP (ApaI at 5′ 111 SbfI Tnos DN ATTATGCCTGCAGGAGCTGGC end) and SbfTnosDN (SbfI at 3′ end) to ATGCAAGCTGTCGAGG generate two PCR products. The two products were fused using outer primers and cloned into pFECT/GFP. pFECT40/GFP/ 112 BsiWI/p19 UP TAATAACGTACGATGGAACG To clone the p19 ORF into p19 AGCTATACAAG pFECT40/GFP/PnosTnos vector. Primer 113 p19SpeI DOWN TTTTTTACTAGTTTACTCG Bsip19UP adds a BsiWI site (underline) CTTTCTTTTTCGAAGG at the 5′ end and primer p19SpeDown adds a SpeI (underline) site at the 3′ end of the ORF. The amplified DNA fragment was cloned into pFECT40/GFP/PnosTnos vector backbone cut with BsiWI and SpeI. pCB/GFP 114 Xba/GFP UP TAAGCATCTAGAATGGCTAGC To clone the GFP ORF into pCB302 AAAGGAGAAGAAC vector. Primer XbaGFPUp adds a 115 GFP/SpeI DOWN TTTTTTACTAGTTTATTTGT XbaI site (underline) at the 5′ end, AGAGCTCATCCA and primer SpeGFPDown adds a SpeI (underline) site at the 3′ end of the ORF

3. pFECT/GFP, pFECT/DsRed, pFECT/HC, pFECT/LC

The cycle 3 GFP gene was PCR mutagenized to be flanked with PacI and AvrII restriction sites on 5′- and 3′-ends, correspondingly. The GFP gene was cloned into the PacI/AvrII sites of the pFECT0, pFECT22 and pFECT40 to obtain pFECT0/GFP, pFECT22/GFP and pFECT40/GFP constructs. DsRed and anti-Langerin antibody light chain and heavy chain genes were subcloned into pFECT vector in the same manner but with only FECT40.

4. FECT/GFP/p19

Nos promoter (Pnos) and nos terminator (Tnos) were used to control the transcription of p19 gene in FECT/GFP/19 binary vector. Pnos/HygR/Tnos in pER8 plasmid was used as template to create two restriction enzyme sites (BsiWI and SpeI) in between Pnos and Tnos, which are cloning sites for p19 insertion. To fuse Pnos and Tnos together, two PCR products were generated for overlapping. The first PCR with Pnos sequence was generated using primer ApaIPnosUP (adds an ApaI site at the 5′ end) and primer PnosBsiWI-overlapDN (adds a BsiWI site and overlap sequence at the 3′ end). The second PCR with Tnos sequence was generated using primer TnosSpeI-overlapUP (adds overlap sequence and a SpeI site at the 5′ end) and primer SbfITnosDN (adds a SbfI site at the 3′ end). The two products were fused using primer ApaIPnosUP and primer SbfITnosDN by overlapping PCR to create Pnos-Tnos fragment (Apap-Pnos/(BsiWI)-(SpeI)/Tnos-(SbfI). Pnos-Tnos PCR product was digested with ApaI and SbfI restriction endonucleases, and then cloned into the FECT/GFP backbone cut with ApaI and SbfI to create FECT/GFP/Pnos-Tnos. To clone the p19 ORF into the FECT/GFP/Pnos-Tnos vector, p19 PCR product was generated using primer BsiWI/p19UP (adds a BsiWI site at the 5′ end) and primer p19SpeI DOWN (adds SpeI site at the 3′ end). P19 PCR product was digested by BsiWI and SpeI and cloned into the FECT/GFP/Pnos-Tnos vector backbone cut with two restriction enzymes to generate FECT/GFP/p19 binary plasmid.

Cloning and Sequencing

The high fidelity polymerase, Phusion (New England Biolabs (NEB), Beverly, Mass.), was used according to company protocols in all constructions. Recombinant clones were introduced into Escherichia coli NEB 10-beta electrocompetent cells by electroporation at 1.44 kV and 129Ω for 5 ms using a BTX 600 Electro Cell Manipulator (BTX Inc., San Diego, Calif., USA) and colonies were screened by PCR using NEB Taq polymerase or by restriction digests of plasmid minipreps prepared by Wizard Plus Miniprep Kit (Promega, Madison, Wis.). Sequence verification was performed using a CEQ capillary sequencer (Beckman Coulter, Fullerton, Calif.).

Agroinfection

Agroinfiltration was performed as described with modifications. Agrobacterium tumefaciens stain GV3101 was used for the agroinoculation of N. benthamiana and cereals. A. tumefaciens was transformed with plasmid constructs using the same conditions as for E. coli above. Agrobacterium transformants were selected at room temperature on Luria-Bertani plates containing 10 μg/ml rifampicin, 25 μg/ml gentamycin and 50 μg/ml kanamycin. A colony of A. tumefaciens was inoculated to 5 ml of L-MESA medium (LB media supplemented with 10 mM MES, 20 uM acetosyringone (Phytotechnology Labs, Shawnee Mission, Kans.), a wound response compound that elicits Agrobacterium virulence, and the same antibiotics), and grown overnight at room temperature. The cells of the overnight culture were harvested by centrifugation and resuspended in induction media (10 mM MES, 10 mM MgCl₂, 100 uM acetosyringone) for a final OD₆₀₀ of 1.0 and incubated for 2 h to overnight at room temperature. The cultures of A. tumefaciens were infiltrated into the underside of leaves of plants with a 3 ml syringe without needle. For agroinoculation of two or more bacterium cultures at the same time, multiple cultures of A. tumefaciens were mixed in equal amounts and infiltrated together. The gene expression or virus activity was tested at 6-8 days post-infiltration and one of three plant replicates were analyzed per experiment.

RT-PCR

To detect FoMV (without GFP or DsRed) in the plant, total RNA was extracted from at after seven days post-inoculation using Tri-Reagent (Sigma, St. Louis, Mo.) according to the manufacturer's protocol. RT-PCR reactions were performed using the RT-PCR kit (NEB, Beverly, Mass.) as described by the supplier. To detect the presence of virus particles, FoMV specific primers were used to amplify the partial viral genome.

GFP and DsRed Photography

Plants were examined under long-wave UV light (UVL-56, UVProducts, Upland, Calif.). For macrophotography, a Canon Digital EOS Rebel XT camera (Canon Inc., Japan) equipped with a Hoya yellow (K2) filter (Hoya Corporation, Japan) was used. For microscopic analysis, samples from infiltrated tissues were mounted with water on a glass slide. Images were obtained with a Nikon TE2000-U inverted microscope, captured using a CoolSnap cf camera (Roper Scientific, Tucson, Ariz.) and analyzed with Metavue imaging software (version 5, Molecular Devices Co, Downingtown, Pa.).

GFP Quantification Assay

GFP fluorescence was analyzed and GFP protein was quantified using a standard curve determined from a purchased GFP standard (Vector Laboratories, Inc, Burlingame, Calif.), since the amount of GFP protein is directly proportional to the fluorescence intensity (Lindbo, 2007a). Total soluble protein extracts were serially diluted in 50 mM carbonate/bicarbonate buffer, pH9.6 and loaded on the 96-well Costar black plate with clear bottom (Costar, Cambridge, Mass.). Fluorescent activities were assayed with a Fluoroskan Ascent FL (Thermo Fisher Scientific Inc., Waltham, Mass.) using a 485 nm excitation and 538 nm emission filter set.

Protein Extraction, SDS-PAGE

Proteins were extracted by grinding agroinfiltrated leaves to a fine powder in liquid nitrogen and mixing 1:2 (w/v) with reducing protein extraction buffer (50 mM Tris, pH7.5, 150 mM NaCl, 0.1% Tween 20, and 0.1% β-mercaptoethanol) or nonreducing protein extraction buffer without β-mercaptoethanol. The insoluble material was removed by centrifugation for 10 min at 16,000×g in a benchtop centrifuge. The supernatant was collected and stored at 4° C. Clarified extract of protein samples were mixed with 3×SDS-PAGE sample buffers (NEB, Beverly, Mass.) and analyzed by PAGE consisting of a 5% stacking gel and a 7.5% or 15% separation gel. Proteins in the gels were identified with Coomassie brilliant blue R-250 (Sigma, St Louis, Mo.).

Western Blot

After electrophoretic separation, the proteins were transferred to a Hybond-P PVDF membrane (Amersham Biosciences, Piscataway, N.J.) using a semi-dry transfer apparatus (Biorad, Hercules, Calif.) at 20 V for 30 min. The membranes were blocked for 1 h with TBST (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.05% (v/v) Tween 20) and 5% (w/v) skimmed milk. Blots were incubated for 1 h with anti-human IgG antibodies conjugated with alkaline phosphatase (Sigma, Saint Louis, Mich.), diluted 1:10000 in TBS with 1% skimmed milk to evaluate the production of the antibody in plants. The enzymatic reaction of alkaline phosphatase was developed with SIGMA FAST BCIP/NBT substrate solution (0.30 mg/ml nitroblue tetrazolium (NBT), 0.15 mg/ml 5-bromo-4-chloro-3-indolyl phosphate (BCIP), 100 mM Tris and 5 mM MgCl₂) (Sigma, St. Louis, Mich.). Apparent molecular weight of proteins was estimated with prestained protein molecular weight markers (NEB, Beverly, Mass.). The anti-Langerin antibody was used as a control in the antibody studies.

Enzyme-Linked Immunosorbent Assays (ELISA)

ELISA 96-well plates (Costar, Nunc, Corning, N.Y.) were coated for 1 h at 37° C. with 2 ug/mL of monoclonal anti-human IgG (Fe specific) (Sigma, St. Louis, Mo.), diluted in 50 mM sodium carbonate buffer (pH 9.6). After three washes with TBS-0.05% Tween 20, the wells were blocked for 1 h at 37° C. with 5% (w/v) skimmed milk in TBST. Plates were loaded with 50 ul of the protein extracts of two fold serial dilution and incubated for 1 h at 37° C. After three washings, the bound recombinant IgG was detected with the specific antigen conjugated with alkaline phosphatase (provided by Gerard Zurawski of the Baylor Institute for Immunology Research, Dallas, Tex.), diluted 1:3000, for 1 h at 37° C., and developed with p-nitrophenyl phosphate (Sigma, St. Louis, Mo.) as substrate. Optical densities were measured at 405 nm on a BIO-TEK ELx800 Universal Microplate Reader (Cole-Parmer, Vernon Hills, Ill.). A standard curve of serial 1:2 dilutions of antibody positive control was included in the experiments, to assess the amount of antibody present in the samples.

Results

Full Length Infectious FoMV cDNA Clone

Full-length FoMV cDNA under transcriptional control of the 35S CaMV promoter was inserted into T-DNA of binary vector JL22 to construct pFoMV (FIG. 1). Agrobacterium stain GV3101 containing pFoMV was agroinoculated in Nicotiana benthamiana to look for symptoms and evidence of viral replication. There were no symptoms of viral infection of FoMV. To detect the presence of FoMV infection, total RNA was extracted from leaves and screened by RT-PCR at 7 days post-inoculation. Systemic movement of viral RNA derived from pFoMV was demonstrated in inoculated plants, but was not seen in uninoculated controls (Data not shown). Thus agroinfection with the pFoMV construct resulted in replication, movement, and production of virions and this FoMV sequence is so mild that no symptoms were produced.

Local Infection of FECT Expression Vector

A. Construction of the Viral Vector pFECT Based on FoMV Genome

The TGB and CP genes in a full-length cDNA clone of FoMV were removed and replaced with restriction sites amenable for inserting heterologous genes. However, the subgenomic promoter of subgenomic RNA1 and the 3′-end of the CP ORF in the FoMV genome were retained to maintain the efficient viral replication in viral vectors, following the design of Komorova et al. (2006), incorporated herein by reference, for PVX, also a potexvirus. The start codon of TGB1 ORF was mutated to prevent expression of TGB1 (FIG. 1). The FoMV triple gene block (TGB) and coat protein (CP) are expressed from 3′-coterminal subgenomic RNAs (sgRNAs). The subgenomic promoters and the transcription start site of the sgRNA1 have not been mapped in FoMV. To ensure the inclusion of the entire functional region of the sgRNA1 promoter, which was expected to extend into the TGB1 ORF, the first 3 (start codon only), 22 and 40 bases of the TGB I ORF were retained to create constructs named pFECT0, pFECT22 and pFECT40, respectively. Thus, the only difference between FECT0/GFP, FECT22/GFP and FECT40/GFP vectors is the promoter length (FIG. 1). FECT0 is the promoter length described in Komorova's paper (2006) for PVX.

To test viral replication and GFP expression of these FECT/GFP vectors, cultures of the GV3101 strain of A. tumefaciens carrying these constructs FECT/GFP were prepared. Leaves of 2-4 week old N. benthamiana were agroinfiltrated with each of the FECT/GFP cultures. At 2-4 days after agroinoculation, GFP-expressing cells could be seen faintly using a hand-held UV lamp and fluorescence microscopy. At this time, there were many faint green spots shown on inoculated leaves on leaves inoculated with FECT40/GFP, many fewer green spots shown for FECT20/GFP, but no green fluorescence could be detected on leaves inoculated with FECT0/GFP. However, the fluorescence was transient and, by eight days post-inoculation, the GFP spots on the FECT22/GFP and FECT40/GFP plants had disappeared. Apparently, the transcription of agroinfiltrated T-DNA induced posttranscriptional gene silencing (PTGS), which led to the inhibition of viral vector infection and the reduction of viral productivity.

B. Application of Gene Silencing Suppressors

It has recently been demonstrated that co-inoculation of RNA-silencing suppressor proteins enhances the expression of heterologous proteins from the viral vectors (Komarova et al. 2006; Lindbo 2007a; Lindbo 2007b). For example, tomato bushy stunt virus silencing suppressor p19 increased 100 times the expression of GFP in tobacco mosaic virus vectors (Lindbo 2007a). To test these suppressors, N. benthamiana plants were agroinfiltrated with a 1:1 mixture of 35S/p19 or 35S/HcPro and FECT/GFP cultures. The accumulation of GFP was followed and imaged with a hand-held UV light and fluorescence microscopy at 3-7 days post-inoculation.

When plants were co-infiltrated with the suppressor, a high level of fluorescence was observed. The fluorescence of the inoculated zones of FECT40/GFP plants was very clearly seen under the UV lamp even with the room lights turned on. Though the amount of GFP-expression was dramatically increased in FECT20/GFP and FECT40/GFP inoculated plants, no fluorescence was seen with FECT0/GFP with or without suppressor co-infiltration. By four days post-inoculation, nearly 90% of the infiltrated area was fluorescent with FECT40/GFP. Also, the leaves with FECT40/GFP displayed much stronger green color than the one with FECT20/GFP. Thus the subgenomic promoter includes at least up to 20 to 40 bases of the ORF.

The unusually high expression level led us to determine the percent of total soluble plant protein that the GFP represented in the inoculated zone. As replication of FECT/GFP replicon progressed, the amount of GFP expressed in the infiltrated leaf increased, so a time course was needed. A. tumefaciens/FECT40/GFP+A. tumefaciens/35S/p19 co-infiltrated leaves from 2 to 7 dpi were homogenized and the relative amounts of GFP in extracts of total soluble protein were measured with SDS-PAGE electrophoresis and coomassie blue protein staining. The GFP was detected from the second day after inoculation. The expression level of fluorescent protein increased gradually, and reached a peak at 7 dpi. At this time it appeared that nearly 100% of the cells in the inoculated leaves were infected with FECT40/GFP mixed with suppressors. GFP accumulated to 30% to 40% of the total soluble protein extracted.

At 7 days post-inoculation it appeared that nearly 100% of the cells in the inoculated leaves were infected with FECT40 mixed with suppressors. Green and red fluorescent cells were observed by fluorescence microscopy in plant leaves agroinoculated with FECT40/GFP or FECT40/DsRed. The FECT vector was able to replicate in the majority of plant leaf cells when delivered by agroinfection. Target protein could be expressed only as the result of this replication and the subgenomic RNA synthesis, in which cell-to-cell movement is not required.

Next compare FECT40/GFP expression was compared to expression obtained by a nonviral 35S construct, since 35S expression is the standard used in plant biotechnology. Gene silencing suppressors can also be used in tandem with 35S promoters directly driving the gene expression of the ORF, without the use of viral vectors. This results in remarkably high protein expression. To make for an exact comparison, the GFP ORF was placed into the same binary plasmid backbone (pCB302) used for FECT40, using the same 35S promoter that drives the expression of the FECT40 viral transcript. A. tumefaciens cultures containing p19 and FECT40/GFP binary constructs were mixed and co-infiltrated into N. benthamiana leaves. Control plants were co-infiltrated with a mixture of Agrobacterium cultures containing either the pCB302/GFP or the 35S:p19 plasmids. Total soluble protein was extracted from infiltrated leaf tissue at seven days post-infiltration. The protein yield of GFP in plants was measured by spectrofluorometry in fluorescence activity assay. The FECT40/GFP vector expressed 1.6 g/kg GFP of fresh-weight tissue, which represented up to 80 times more GFP than was obtained from co-infiltrating T-DNAs for 35S:GFP and 35S:p19 into plants. In multiple repetitions of this experiment, the FECT system consistently expressed significantly more GFP (1.58±0.13 g/kg) than the non-viral transient expression systems examined (0.02±0.002 g/kg).

Because the TGB and CP of FoMV is required for systemic and cell-to-cell movement, the FECT viral vectors were not expected to move systemically and cell-to-cell in plants. To test this, N. benthamiana plants were inoculated with either JL24, a full length TMV vector which expresses GFP, or FECT40/GFP by agroinfection mixed with p19. When leaves were infiltrated with higher concentration of JL24 or FECT/GFP containing agrobacterium, almost all plant cells in the infiltrated area expressing GFP made it difficult to separate an individual focus. Serial dilution experiment of agroinfection was performed on N. benthamiana plants. Plants were observed under UV illumination to visualize GFP expression and, hence, viral movement. The vector JL24 expressed GFP and all of the genes of TMV, including the MP (corresponding for TGB in FoMV) and the CP (corresponding for CP in FoMV), and was observed to move cell-to-cell at 4 dpi and systemically at about 7 dpi. As TMV replicates and viral particles move cell-to-cell from inoculated cell to adjacent cells through the help of MP, individual GFP-expressing foci enlarge it. The FECT replicon was never observed to move systemically in the agroinoculated plants in this or any other experiment, and the green fluorescent loci on the leaves never grew to larger spots by cell-to-cell movement. This effect was especially clear in comparing the sizes of individual GFP-expressing cell foci in 4 dpi images of leaves infiltrated with 1:1000 dilutions of FECT/GFP and 1:100 JL24. In this case, the spots were well separated and no cell to cell spread was observed beyond that which occurred initially.

C. FECT Expression Analysis in Monocots

It was demonstrated agroinoculation of FECT vector together with a silencing-suppressor gene dramatically increases the production level of target protein in N. benthamiana plants. The host range in of FECT in grasses, its natural hosts, was investigated in the same method. Switchgrass, foxtail millet, barley, wheat, oat and corn were co-agroinoculated with the mixture of two Agrobacterium cultures containing FECT40/GFP and p19, respectively. Fluorescing cells were observed in corn's leaves agroinoculated with FECT/GFP by fluorescence microscopy, but not in uninoculated control leaves. In barley, clumps of cells were very occasionally seen that were not found in controls. Single fluorescent cells were present in oats and other grasses, but there were also these kinds of fluorescing cells in noninfected leaves. The low transformation efficiency in monocots via agroinoculation made it difficult to conclusively distinguish between autofluorescence in control leaves and GFP fluorescence in inoculated leaves. Successful reports of grass species agroinoculation were not found by the authors except for a single report of the infection of scattered single GUS-expressing transformed cells of agroinoculated switchgrass.

D. FECT Expression Analysis in Legumes

Expression of GFP by FECT/GFP was apparent in at least four species of legumes tested. GUS expression was visualized colorimetrically in bean and cowpea and GFP expression was visualized by fluorescent microscopy for Medicago trunculata and lentil, with large numbers of cells fluorescing, in clear distinction from uninoculated leaves.

E. Effect of Gene Silencing Suppressor in Cis Construct

High yield protein production in N. benthamiana demonstrates that specific interaction between the suppressor and FECT viral vector is absolutely required for gene silencing suppression. However, only a small fraction of cells, at best, are expected to be infected by Agrobacterium in the agroinoculation of grasses. As the trans construct, p19 has to be expressed in a separate binary vector and two agrobacterium cultures have to be mixed up before agroinoculation. Because of expected low rates of infection, co-agroinfection of the same cell with FECT and p19 was considered almost impossible in grasses. So, a combined FECT/p19 construct was built for the co-expression of p19 and FECT in the same cell. The p19 ORF was cloned into the FECT/GFP vector under the control of the nos promoter and nos terminator. GFP expression was examined under a hand-held UV lamp at 2 days post-inoculation in N. benthamiana. There was no significant difference between cis and trans p19 construct, with both showing strong fluorescence in the agroinoculated zone. The only difference was seen at seven days post-inoculation, when the trans treatment gained in fluorescence while the cis treatment remained at the same level.

F. Transient Antibody Expression with FECT Viral Vector

The FECT vector has been successfully used to express glucuronidase (GUS; data not shown), DsRed and GFP in N. benthamiana. To expand the repertoire of genes that could be expressed, a very large and multimeric protein was chosen. cDNA clones of anti-langerin mAb IgG4 HC and LC were prepared by PCR introducing restriction cloning sites for PacI and AvrII at the 5′ and 3′ ends, respectively. The gene fragments encoding HC and LC were cloned into viral vector FECT40, under the control of the subgenomic promoter for FoMV TGB I mRNA, obtaining FECT40/LC and FECT40/HC. N. benthamiana plants were co-agroinfiltrated with three Agrobacterium mixtures carrying the antibody expression constructs —FECT40/LC and FECT40/HC- and gene silencing suppressor p19 driven by 35S.

Infected leaves of N benthamiana were homogenized in extraction buffer, centrifuged to clear the supernatant, and directly coated onto ELISA plates. Plant-based recombinant antibody bound to the antigen was detected using the Langerin alkaline phosphatase conjugate. Extracts from plants infected with FECT40/GFP were used as negative controls. The ELISA results demonstrate that the total soluble protein from agroinfiltrated leaves contained molecules which human heavy and light antibody chains where assembled. Western blot analysis of total soluble protein extracted by non-reducing conditions indicated that the protein material from transient expression contained a 170 kDa full-length antibody protein band of similar molecular size as the positive control antibody which is expressed by mammalian expression system. The total soluble protein from leaves agroinfiltrated with Agrobacterium tumefaciens with FECT empty vector plasmid was negative by ELISA and western blot, as expected. The antibody yield was 10 μg/g fresh weight of agroinfiltrated leaves as calculated by ELISA using the standard antibody standard curve.

Discussion

Very high protein expression rates were demonstrated in N. benthamiana for the deleted viral vector, FECT. At 40% TSP for the expression of GFP, this vector expresses at rates equivalent to any plant expression system available and well beyond expression rates published for traditional plant virus vector systems. The GFP expression of the best nonviral 35S system is 270-340 ug GFP/g fresh tissue aided by p19 and 5-12 ug/g without p19. This compares to the observed expression of 1.6 mg/g. Thus, a vector system has been developed which expresses protein at close to the biological limits for plant cells.

The FECT viral vector system has many features that enhance its environmental safety when used via agroinoculation or potentially as a transgene. First, its genome is reduced by more than half, making it several crippled. Second, it does not replicate efficiently unless the plant immune system is suppressed. Thus, if it were to somehow infect another plant (e.g., via its Agrobacterium carrier), it would replicate poorly. Third, it lacks a coat protein and cannot form a virion, making it impossible for the virus to survive outside of a host. Finally, it is derived from a virus that in most hosts causes only mild infections. In fact, no symptoms were observed in N benthamiana with the full length virus.

A novel and useful control mechanism operational with the FECT construct. In the absence of a silencing suppressor, almost no expression of GFP occurred, and what expression did occur was transient, disappearing by the seventh day after inoculation. This contrasts with the extreme expression in the presence of the silencing suppressor. This was not the case with the PVX vector of Komorova et al. (2006). Though PVX and FoMV are both potexviruses, the Komorova deletion vector performed fairly well even in the absence of suppressor. This paper states that no extra bases of ORF were used to extend the subgenomic promoter, however it was found that no expression occurred when this was emulated with FoMV. Only when extra bases of the TGB1 ORF were included was expression observed, with or without suppressor. Thus, the vectors differed in design as well as performance.

The effect of removing the coat protein of TMV (tobamovirus family) and portions of the movement protein have been examined previously by others. Complete removal of the movement protein produced only small infection points, which could be rescued by the co-agroinoculation of p19 or of various sized portions of the TMV movement protein. Thus, a similar effect was found in the tobamoviruses as was found in the current work with the FoMV potexvirus. It would not be expected that that the unrelated coat proteins and movement protein(s) of tobamoviruses and potexviruses would provide the same on/off effect with regard to the presence of suppressors. Not only are the coat proteins unrelated in sequence, but there are three triple gene block proteins responsible for movement rather than the single protein for TMV. Indeed, the work of Komorova et al. (2006) appeared at that time to clearly demonstrate that, for potexviruses, the removal of coat protein and triple gene block genes produced a vector which was quite functional in the absence of suppressor. The present results were thus unexpected, and are perhaps due to the nature of FoMV itself.

The FECT system was able to express a fully multimeric and immunological detectable IgG. The yield for this antibody was calculated to be 10 ug/g fresh tissue, which is 50-fold less than the recently published dual-virus technique of ICON Genetics, but is at least comparable to the yield obtained with nonviral systems. The low yield of multimer is probably due to less than optimal co-infection of cells with both the FECT/HC and FECT/LC viruses.

There are several uses for the use of FECT vectors. This system has the capacity for high level expression of a variety of proteins, including GFP (0.7 kb and the larger GUS (1.8 kb) and the multimeric Ds-Red (0.7 kb) proteins. At low levels, FECT was shown to express properly assembled antibody. This system, then, would be expected to be amenable to the production of vaccines or other pharmaceutical or industrial proteins via agroinoculation. The tight on/off control of this system also makes it suitable for an inducible transgenic system from the perspective of environmental safety, high yield, and the expression of proteins toxic to the plant host.

Example 2 Plants

Seeds of Nicotiana benthamiana, Vigna unguiculata (cowpea) and Phaseolus vulgaris (Pinto bean), Lens culinaris (lentils), Pisum sativum (peas) and Medicago trunculata (a model legume plant) were sown in Sunshine Mix #1 and plants were grown in 4″ pots at 23° C. with 24 hour illumination. N. benthamiana plants were agroinoculated at the 5-10 cm stage. Legumes were agroinoculated at the two to four week stage with fully expanded primary or secondary leaves.

SHMV cDNA Constructs

All SHMV clones used in this study are the derivatives of a wild-type SHMV cDNA clone (SEQ ID NO:13; Silver et al., 1996) and were constructed using standard recombinant DNA techniques. The SHMV comprises a 5′ UTR (SEQ ID NO:8), a replicase ORF (SEQ ID NO:9), a movement protein ORF (SEQ ID NO:10), a virus coat protein ORF (SEQ ID NO: 11), a 3′ UTR (SEQ ID NO:12). The SHMV sequence was obtained from Dr. C. M. Deom, University of Georgia, Athens, Ga., USA. The high fidelity polymerase, Phusion (NEB, Beverly, Mass.), was used according to company protocols for PCR. Recombinant DNA was introduced into E. coli 10-beta electrocompetent cells (NEB, Beverly, Mass.) and screened by PCR using Taq polymerase (NEB, Beverly, Mass.) or restriction digest and then sequenced using a CEQ capillary sequencer (Beckman Coulter, Fullerton, Calif.).

1. pSHMV

The binary vector, pJL22 (Lindbo, 2007a), has the mini binary plasmid, pCB301, as backbone. JL22 has a multiple cloning site flanked by a CaMV 35S promoter and a CaMV 3′ polyA signal/transcription terminator. SHMV full length viral cDNA (Silver et al., 1996) and a ribozyme sequence from JL24 (Lindbo, 2007a) were inserted into the MCS of pJL22. SHMV in viva transcripts should be processed by the ribozyme to generate authentic SHMV 3′ ends. This full viral expression cassette, including promoter and terminator, is flanked with the left and right borders of the T-DNA (FIG. 2).

2. pSHacgCP

The use of overlap PCR allowed the double start codons at the beginning of coat protein ORF in pSHMV to be functionally eliminated by mutation to a pair of ACGs. The two primers (dCP-SHMV Up and dCP-SHMV Down) in the initial PCR of the overlap strategy were used to mutate ATGATG to ACGACG without a change in protein sequence of the movement protein ORF in pSHMV. These were mated with the downstream primer, JL22 RB Down (SEQ ID NO:89), and the upstream primer, SHMV 4658 Up, respectively, in the initial PCR and were used as a pair for the second (overlap) PCR. The overlap PCR product was cloned back into KpnI/PmeI cut pSHMV to make pSHacgCP.

3. pSHEC

Mutagenic PCR was performed to delete the CP ORF and introduce PacI and BssHII cloning sites for foreign genes. These sites were introduced using two primers, SHMV PacBss3UTR Up and JL22 RB Down. The PCR product (comprising the 3′ UTR and the terminator, ribozyme and T-DNA right border) was cut with PacI/PmeI and cloned into the generic cloning vector pNEB193. Next, three lengths of subgenomic promoter were retained to drive foreign genes instead of the CP gene. Specifically, three downstream primers (SHMV Pac5838 Down, SHMV Pac5854 Down and SHMV Pac5869 Down) were designed to retain 58 nts, 74 nts and 89 nts of the 5′ end of the CP ORF sequence, respectively. These were each paired with the upstream primer, SHMV 4658 Up, as above and the PCR products were each cloned into the KpnI/PacI site of pNEB293 already carrying the 3′UTR and downstream elements. Finally, the KpnI/PmeI fragment was transferred from pNEB193 to pSHacgCP to create SHEC58, SHEC74 and SHEC89.

SHEC74 vector (SEQ ID NO:55) comprises a 5′ UTR (SEQ ID NO:43), a replicase ORF (SEQ ID NO:44), a movement protein ORF (SEQ ID NO:45), the initial 74 by of coat protein with first two codons mutated (ATG->ACG) (SEQ ID NO:46), PacI/Bss HII cloning site and 3′ UTR (SEQ ID NO:47), 35S terminator (SEQ ID NO:48), miscellaneous sequence (SEQ ID NO:49), T-DNA right border (SEQ ID NO:50), JL22 sequence (SEQ ID NO:51), T-DNA left border (SEQ ID NO:52), miscellaneous sequence 2 (SEQ ID NO:53), and a 35S promoter (SEQ ID NO:54).

4. pSHEC/GFP and pSHEC/GUS

The Cycle 3 GFP gene was PCR amplified to add Pact and BssHII sites and cloned into the PacI/BssHII sites of pSHEC58, pSHEC74 and pSHEC89 to obtain pSHEC58/GFP, pSHEC74/GFP and pSHEC89/GFP. In the same way, GUS (the E. coli uidA gene) was subcloned into pSHEC74 to form pSHEC74/GUS construct.

5. pSHAC/GFP

pJL24 (Lindbo, 2007) is a TMV vector with the CP subgenomic promoter, CP ORF, and 3′UTR of the Tobamovirus, Tobacco mild green mosaic virus (TMGMV) to prevent recombination with the TMV subgenomic promoter driving the foreign gene. The GFP, CP subgenomic promoter and CP ORF of pJL24 were PCR amplified and the PCR product was cloned into the PacI/BssHII sites of the pSHEC74 to generate pSHAC74/GFP construct.

SHAC74 vector (SEQ ID NO:72) comprises a 5′ UTR (SEQ ID NO:56), a replicase ORF (SEQ ID NO:57), a movement protein (SEQ ID NO:58), the initial 74 by of coat protein ORF with the first two codons mutated (ATG->ACG) (SEQ ID NO:59), PacI and AvrII cloning sites (SEQ ID NO:60), a TMV-UI 3′ UTR (SEQ ID NO:61), a Tobacco mild green mottle virus subgenomic promoter (SEQ ID NO:62), a Tobacco mild green mottle virus CP ORF (SEQ ID NO:63), a SHMV 3′ UTR (SEQ ID NO:64), a 35S terminator (SEQ ID NO:65), a miscellaneous sequence (SEQ ID NO:66), a T-DNA right border (SEQ ID NO:67), JL22 sequence (SEQ ID NO:68), T-DNA left border (SEQ ID NO:69), miscellaneous sequence 2 (SEQ ID NO:70), and a 35S promoter (SEQ ID NO:71).

6. 35S/GUS

To clone the GUS ORF into the generic binary vector, pCB302 (Xiang et al., 1999), primer XbaGUSUp was used to add aXbaI site at the 5′ end, and primer SpeGUSDown was used to add a SpeI site to the 3′ end of the GUS ORF. The PCR product was cloned into the XbaI/SpeI sites of the pCB302 to generate pCB/GUS.

7. pSHEC74/GFP 15CP3′ and pSHEC74/GFP 40CP3′

In these constructs, 15 or 40 by of the 3′ end of the ORF of CP were reintroduced in an attempt to improve translation, following the design of the TMV TRBO vector (Lindbo, 2007b). A PCR product was generated using upstream primer BssSHMVUp15 or BssSHMVUp40 and downstream primer JL22 RB Down. The amplified DNA was cloned into pSHEC74/GFP cut with BssHII and PmeI.

TABLE 2 Primers used for plasmid construction SEQ ID Oligonucleotide Plasmid Primer NO sequence (5′-3′) Purpose pSHacgCP SHMV 4658 Up 116 CAGATATCCAATCGGTCTCC To generate a mutation in the (pSHMV nt. 4597- AACAA initiation codon of the CP cDNA 4621) and eliminate the double ATG's dCP-SHMV Down 117 TCGGAATCGAGTATGCCGTC start codon within pSHMV. The (pSHMV nt. 5769- GTCAAATACAGAC mutation is in underlined. 5801) dCP-SHMV Up 118 GTCTGTATTTGACGACGGCA (pSHMV nt. 5769- TACTCGATTCCGA 5801) JL22 RB Down 119 TCTAATAAACGCTCTTTTCT (pSHMV nt. 6874- TCTTAGGTT 6901) pSHEC58 SHMV Pac5838 Down 120 TGGAATTTAATTAACGTAAT Three downstream primers pSHEC74 (pSHMV nts.5851- TTTCAGTAAA (containing the rare-cutting PacI) pSHEC89 5822) were paired with the primer - SHMV Pac5854 Down 121 AACCTATTAATTAATGGAAT SHMV 4658 Up - as above to save (pSHMV nts.5865- GTAATCAGCG 58 nts, 74 nts and 89 nts 5′ end of 5836) CP DNA sequence from mutated SHMV Pac5869 Down 122 CTGCGTTAATTAATCAACCT start codon of coat protein (pSHMV nts.5880- ATTAACAAATG respectively. PacI and BssHII 5850) cloning sites were introduced by SHMV PacBss3UTR 123 TGCTCGTTAATTAAACTGCG PCR amplified with two primers Up CGCTCTAGTGTAAAAGTTTG (SHMV PacBss3UTR Up and JL22 (pSHMV nts 6275- GTC RB Down). Once each pair of PCRs 6292) is completed, they are cut with KpnI/PacI or PacI/PmeI and cloned into pSHacgCP vector backbone cut with KpnI and PmeI to create pSHEC58, pSHEC74 and pSHEC89. pSHEC58/GFP PacGFPUp 141 TTGTCATTAATTAAGCTAGC To clone the GFP ORF into the pSHEC pSHEC74/GFP AAAGGAGAAGAAC vector. Primer PacGFPUp adds a PacI pSHEC89/GFP GFPBssDown 124 TTTACTCCTAGGTTATTTGT site (underline) at the 5′ end, and AGAGCTCATCCA primer GFPBssDown adds an BssHII  site (underline) to the 3′ end. pSHEC74/GUS PacGUSUp 125 GGATGGTTAATTAAATGTTA To clone the GUS ORF into pSHEC CGTCCTGTAGAAAC vector. Primer PacGUSUp adds an GUSBssDown 126 TTTACTGCGCGCTCATTGTT PacI site (underline) at the 5′ end, TGCCTCCCTGC and primer BssGUSDown adds an BssHII (underline) site at the 3′ end  of the ORF. pSHAC/GFP PacGFPUp 141 TTGTCATTAATTAAGCTAGC GFP gene and coat protein (CP) AAAGGAGAAGAAC gene of Tobacco Mild Green TMGMVCPBssDown 127 TTTACTGCGCGCCTAAGTAG Mosaic Virus (TMGMV) were CCGGAGTTGTG amplified together with JL24 as the template. The amplified DNA fragment was cloned into the PacI/BssHII sites of the pSHEC74 to generate pSHAC74/GFP constructs. pSHEC74/GFP BssSHMVUp15 128 TTTACTGCGCGCCCACGTAC To add a 15 bp or 40 bp more to the 15CP3′ (pSHMV nts 6235- CGCTTAGTCTAG 3′ end of CP in pSHEC74 vector. 6255) The PCR product was generated pSHEC74/GFP BssSHMVUp40 129 TTTACTGCGCGCTCTGACAT using primer BssSHMVUp15 or 40CP3′ (pSHMV nts 6235- GGTTGGTGACAAC BssSHMVUp40 with a BssHII site  6255) (underline) at the 5′ end and primer JL22 RB Down at downstream of PmeI site in T-DNA right border of pSHMV. The amplified DNA fragment was cloned into pSHEC74/GFP vector backbone cut with BssHII and PmeI. pCB/GUS XbaGUSUp 130 GGATGGTCTAGAATGTTACG To clone the GUS ORF into pCB302 TCCTGTAGAAAC vector. Primer XbaGUSUp adds a SpeGUSDown 131 TTTACTACTAGTTCATTGTT XbaI site (underline) at the 5′ end, GCTGCCTCCCT and primer SpeGUSDown adds a SpeI (underline) site at the 3′ end  of the ORF.

Agroinoculation of Plants

Binary constructs were transformed into A. tumefaciens EHA105 by electroporation at 1.44 kV and 129Ω for 5 ms using a BTX 600 Electro Cell Manipulator (BTX Inc., San Diego, Calif., USA). A. tumefaciens transformants were selected with 10 μg/ml rifampicin and 50 μg/ml kanamycin (Phytotechnology lab, Shawnee Mission, Kans.). Initially, three transformants per binary vector construct were tested for agroinoculation of plant leaves. The gene expression or virus activity was tested at 6 and 8 days post-inoculation and one of three transformants was used for further experimentation.

Agroinoculation was carried out according to standard procedures. A two-day colony of A. tumefaciens was transferred to 5 ml LB media supplemented with 10 mM MES (Fisher Biotech,), 20 uM acetosyringone (Phytotechnology lab, Shawnee Mission, Kans.), 10 ug/ml rifampicin and 50 ug/mL kanamycin, and grown overnight at 24° C. The cells of the overnight culture were collected by centrifugation, resuspended in induction media (10 mM MES, 10 mM MgCl₂, 150 uM acetosyringone) for a final OD₆₀₀ of 1.0 and incubated for 2 h to overnight at room temperature. The cultures of A. tumefaciens were infiltrated with a 3 ml syringe without needle at the abaxial leaf surface.

RT-PCR

Total RNA was extracted from leaves after seven days post-inoculation using Tri-reagent (Sigma, St. Louis, Mo.) according to the manufacturer's protocol. RT-PCR reactions were performed using an RT-PCR kit (NEB, Beverly, Mass.), as described by the supplier, using SHMV-specific primers.

Electron Microscopy

Virus samples were prepared for transmission electron microscopy using a leaf dip method. Hexagonal 300 mesh copper grids (Electron Microscopy Sciences, Hatfield, Pa.) were coated with a film made from a 1% (w/v) aqueous formvar solution. A drop of a saturated aqueous uranyl acetate stain was placed on the coated grid. The cut edge of the leaf was pulled through the drop of stain several times to release virus particles. After 1 minute, the stain was removed with filter paper and the grid was allowed to dry. Samples were viewed using a JEOL JEM 1010 Transmission Electron Microscope (JEOL Ltd., Tokyo, Japan) operated at 60 kV.

Protein Extraction and SDS-PAGE

Inoculated N. benthamiana leaf tissue (1 g) was ground to a fine powder in liquid nitrogen using a pestle and mortar. The powder was resuspended by vigorous mixing in 2 ml of protein extraction buffer (50 mM Tris, pH7.5, 150 mM NaCl, 0.1% Tween 20, and 0.1% 3-mercaptoethanol). Extracts were centrifuged for 15 min at 13,000×g at 4° C. Clarified supernatant was stored at 4° C. Clarified extracts of protein samples were mixed with 3×SDS-PAGE sample buffer (NEB, Beverly, Mass.) and PAGE analyzed on a 5% stacking gel and 15% separation gel. Gels were stained with Coomassie brilliant blue R-250 (Sigma, St Louis, Mo.) to visualize proteins.

Detection of GFP Fluorescence

Plants were examined under long-wave UV light using a hand-held UV device (UVL-56, UV Products, Upland, Calif.) and photographs were taken with Canon digital EOS Rebel camera equipped with a Hoya yellow (K2) filter (Hoya Corporation, Japan). For GFP-positive plants, samples from infiltrated tissues were mounted with water on a glass slide. Images were obtained with a Nikon TE2000-U inverted microscope, captured using a CoolSnap cf camera (Roper Scientific, Tucson, Ariz.) and analyzed with Metavue imaging software (version 5, Molecular Devices Co, Downingtown, Pa.).

Histochemical GUS Assay

X-Gluc substrate solution was made with 1 mM X-Gluc (5-bromo-4-chloro-3-indolyl-β-D-glucuronic acid, Gold Biotechnology, St. Louis, Mo.), 100 mM sodium phosphate buffer, pH 7.0, and 0.5 mM potassium ferrocyanide (Acros Organics, Morris Plains, N.J.). Seven dpi leaves were placed in X-Gluc solution and were subjected to a 700-mm Hg (93 kPa) vacuum for 5 min to improve the penetration of the substrate. The samples were incubated in the dark at 37° C. from 1 h to overnight until the staining was satisfactory. After staining, the leaves were cleared with 70% ethanol to improve contrast by removing photosynthetic pigments. GUS-stained leaves were viewed under a light microscope. Micro and macrophotography was performed as above but without UV light.

Spectrophotometric GUS-Assay

Transient GUS activity was determined using the spectrophotometric GUS assay. Inoculated leaves were harvested and grinded as frozen tissue in liquid nitrogen. Freshly prepared 1 ml of GUS lysis buffer (50 mM NaPO₄ pH 7.0, 10 mM β-mercaptoethanol, 0.1% Triron X-100) was added to ground tissue powder. Crude extracted homogenate was centrifuged in a microcentrifuge at 12,000×g for 5 min and the extract supernatant was collected. Lysis buffer (100 ul of 10 mM p-nitrophenyl beta-D-glucuronide (PNPG, Sigma)) was added and the reaction was allowed to proceed at 37° C. for 15 h. The reaction was terminated by the addition of 0.4 ml 2.5 M 2-amino-2-methyl propanediol (Sigma), followed by measurement of the absorbance at 415 nm.

Results

Full Length Infectious SHMV cDNA Clone

Full-length SHMV cDNA under transcriptional control of the 35S promoter was inserted into the T-DNA of binary vector JL22 to construct pSHMV (FIG. 2). Agrobacterium stain EHA105 containing pSHMV were agroinoculated in Nicotiana benthamiana and various legumes to verify host range. Systemic symptoms were visible as mild leaf distortion and mottling in cowpea, and some necrotic spots in Pinto bean and strong mosaic and distortion in N. benthamiana similar to TMV infection, while later symptoms involved more severe leaf distortion in systemically-infected leaves in cowpea and bean. SHMV RNA was detected in the inoculated and systemic leaves of these legumes by RT-PCR. As confirmation, SHMV virions were seen in systemic leaves with a transmission electron microscopy, which showed an abundance of rod-shaped virions typical of tobamovirus infections.

Infection of N. benthamiana by SHEC Variants 1. Construction of pSHEC

A CP-deletion vector was constructed to allow the environmentally safe expression of protein via agroinoculation or in transgenic plants. The coat protein (CP) subgenomic promoter would be used to drive foreign gene expression and it was expected to comprise sequence both upstream and downstream of the start codon of CP ORF. Since there was an additional AUG next to the start codon, both of the codons were mutated to ACGs (SHacgCP construct) so that the start codon of the foreign gene would be used. Next, constructs with varying lengths of putative subgenomic promoter were created, including 58, 74 and 89 nts of CP ORF in constructs SHEC58, SHEC74 and SHEC89, respectively. Thus, these vectors differed from pSHMV only in the mutated AUGs, a PacI/BssHII cloning site, and the elimination of the CP ORF except for the upstream bases noted. GPF was inserted into the cloning site of each construct to create the SHEC/GFP series.

To test the expression of the SHEC/GFP vectors, cultures of the EHA105 strain of A. tumefaciens with SHEC/GFP were prepared and N. bethamiana plants were agroinoculated. Four days post-inoculation (dpi), GFP-expressing cells could be seen using a hand-held UV lamp and fluorescence microscopy. There are many green spots shown on inoculated leaves and no significant differences of GFP expression between these SHEC/GFPs.

2. Co-Inoculation with Gene Silencing Suppressors P19 and HcPro

Co-inoculation of RNA-silencing suppressor proteins has enhanced the expression of heterologous proteins from the vectors (Komarova et al. 2006; Lindbo 2007a; Lindbo 2007b). Tomato bushy stunt virus silencing suppressor p19 increased 100 times the expression of GFP in TMV vectors (Lindbo 2007a). HC-Pro, from Tobacco etch virus, serves a similar function in suppressing gene silencing. To test two gene silencing suppressors, N. benthamiana plants were agroinoculated with a 1:1 mixture of 35S/p19 or 35S/HcPro and pSHEC/GFP cultures. The accumulation of GFP was followed and imaged by hand-hold UV light and fluorescence microscopy at 3-7 days post-inoculation. When plants were infiltrated with virus and either of these two gene silencing suppressors, the amount of GFP-expression was dramatically increased. At 7 dpi the great majority of the cells fluoresced strongly.

3. Determining Protein Yield of SHEC

A. tumefaciens/pSHEC78/GFP+A. tumefaciens/35S:p19 co-infiltrated leaves from 3-7 dpi were extracted and the relative GFP expressions were examined by SDS-PAGE electrophoresis and coomassie blue staining. Recombinant GFP expression in infiltrated leaves increased up to the maximal GFP expression level at 7 dpi, to 25% total soluble protein as measured in comparison to a known quantity of GFP protein standard and the determined total protein content of the sample.

4. 3′-Terminal Sequences of Coat Protein Gene

The 3′-terminal 22 nt of the TMV CP ORF as a UTR downstream of the GFP ORF have a positive effect on GFP accumulation (Lindo 2007b). However, with the last 3′-terminal 50 nt of the CP ORF as a UTR downstream of the GFP ORF, GFP accumulation decreased by 70%. To further elucidate possible up-regulatory roles of specific sequences from the 3′ end of CP ORF, constructs were made adding either 15 nt or 40 nt sequences derived from the 3′ termini of the CP ORF of SHEC74/GFP, creating 5′ GFP-15 3′ or 5′ GFP-40 3′ constructs respectively. However, these 3′ ORF additions did not significantly increase the GFP accumulation level in N. benthamiana compared with SHEC74, which lacked any 3′ CP ORF sequence.

5. Cell-to-Cell Movement of SHEC Expression Vector

When the CP genes of TMV, PVX, Brome mosaic virus (BMV), and Cowpea mosaic virus (CPMV) were replaced with the GFP encoding sequence, the chimeric viruses were restricted to local GFP expression (Lindbo 2007b; Komarova et al. 2006). With the SHEC vectors, lacking a CP ORF, no green spots were found in systemic leaves, only in the inoculated leaves. Fluorescence was seen to move into the petioles and stems over several weeks, presumably by cell-to-cell movement through the parenchyma rather than through the phloem since no vein banding patterns typically seen with systemic infections were ever seen in SHEC/GFP infected plants.

SHEC Expression in Legumes

Pinto bean and cowpea were co-inoculated with a mixture culture of agrobacterium containing SHEC74:GFP and 35S:p19 and examined by fluorescence microscopy. Though no fluorescence was seen macroscopically, inoculated Pinto bean leaves showed unique and bright fluorescent cells under the fluorescence microscope, in contrast to uninoculated Pinto bean leaves, which were uniformly dark. Unfortunately, uninoculated control cowpea leaves had many autofluorescent cells, but it appeared that inoculated leaves had some unique fluorescent cells not present in uninoculated controls.

SHEC containing the β-glucuronidase (GUS) gene, in co-agroinoculation with 35::p19, yielded legume infections that showed strong GUS expression macroscopically for Pinto bean and cowpea as well as for N. benthamiana and also for Medicago trunculata, showing large patches of blue pigment, the product of the GUS enzyme reacting with the X-gluc substrate. These blue patches were somewhat less prominent for pea and lentil. When Pinto bean, cowpea and N. benthamiana infections were examined microscopically, all showed large numbers of dark blue cells. To verify the absence of endogenous GUS activity, A. tumefaciens/pSHEC78/GFP was used as the negative control. To compare SHMV expression vector with other transient expression systems, A. tumefaciens cultures with plasmids pCB/GUS or 35S/p19 were mixed and co-infiltrated into N. benthamiana leaves. The activity levels of GUS in extracts were determined by a spectrophotometric GUS assay. SHEC/GUS expression was five times that of the 35S::GUS in the pCB/GUS construct co-infiltrated with the 35S::p19 gene in both N. benthamiana and legume. GUS expression was very low when legumes were agroinoculated with SHEC/GUS in the absence of 35S::p19. As a negative control, agrobacterial cultures carrying SHEC/GUS did not by themselves produce any blue color by the GUS assay in the absence of inoculation onto plants.

The Full Length Vector, SHAC/GFP

To rescue SHEC vector for systemic movement, the pSHAC78/GFP was constructed. The CP gene of the TMV and SHMV relative, TMGMV, together with its subgenomic promoter, was inserted upstream of the 3′ untranslated region (UTR) of pSHEC74/GFP to compensate the function of SHMV CP. The additional sequences of 5′ end of SHMV CP ORF were reserved as the subgenomic promoter to drive GFP expression as in SHEC74. Using a different tobamoviral CP subgenomic promoter was expected to prevent homologous recombination between duplicated homologous subgenomic promoters which would lead to deletion of the foreign gene. The SHAC vector expressed GFP plus all of genes for viral functions, including the MP, CP and replicase. Green fluorescent spots were observed in locally inoculated leaves at three dpi, and moved systemically to uninoculated leaves at about seven days post-inoculation. To monitor the stability of foreign gene expression in the recombinant viral vector, vSHAC74/GFP was serially passaged in N. benthamiana every 20-30 days intervals using sap inoculation. This chimeric SHMV had no disease symptoms during the infection of plants and the GFP expression was stable for three months over four serials passages using sap inoculation.

However, SHAC/GFP did not move and express GFP systemically in legumes. When Pinto bean was co-inoculated with the mixture culture of agrobacterium containing SHAC/GFP and 35S:p19, green fluorescence was observed only in the inoculated leaves of the plant by fluorescent microscopy. GFP expression was not able to be found in upper leaves of legumes, and the genomic RNA of SHMV was not detected in systemic leaves by RT-PCR. SHAC/GUS was not constructed.

Discussion

Currently, vectors derived from the type virus of the Tobamovirus family, TMV, using the host N. benthamiana, dominate the commercial use of plant virus vectors for the production of pharmaceutically relevant proteins. A TMV vector which has been heavily modified with added introns to increase nuclear export of the viral transcript has been developed, resulting in foreign protein expression yields of up to 25% total soluble protein (Gleba et al., 2005). Fraunhofer does not use added introns in their TMV vectors, but have made other modifications. Previous to this, many modifications were made to create an earlier generation TMV vector. Thus, the current commercial TMV vectors represent a series of improvements over the original vector.

Herein, the use of the Tobamovirus, SHMV, as a plant expression vector for use in N. benthamiana and legumes has been initiated. An infectious clone was obtained from Mike Deom of the University of Georgia (unpublished) which was from the virus used in determining the SHMV 5′ sequence (Silver et al., 1996). Realizing that the production of an excellent full length vector will be a long term process, as it was for TMV, a vector suitable for agroinoculation and for use in stable transgenics was developed. For these purposes, the coat protein gene is not necessary, freeing up a subgenomic promoter for expression of a foreign gene and simplifying the vector development process.

The effect of additional bases from the 5′ and 3′ ends of the CP ORF on expression of GFP was examined. It was established that a subgenomic promoter comprising 58 bases of CP 5′ ORF was as effective as longer promoter constructs in the expression of GFP. This is in accordance with previous studies on TMV. The minimal TMV CP subgenomic promoter was mapped between −69 and +12, whereas the boundaries of the fully active promoter were between −157 and +54. Also, it was found that the addition of 15 or 40 bases from the 3′ end of the CP ORF did not improve GFP expression, in contrast to the report for the TMV-based TRBO vector (Lindbo, 2007b).

The use of gene silencing suppressors provides a strong on/off effect with the entire SHEC vector series. In N. benthamiana, GFP expression was very weak in the absence of suppressors, but strong in the presence of either p19 or HcPro. In both N. benthamiana and in legumes, there is little GUS expression in the absence of p19, but in the presence of p19, GUS production was very strong. This on/off property would be useful in an inducible transgenic system. The control of both the suppressor gene and the viral construct by inducible promoters would be expected to provide less leakiness than control of the viral construct alone. In addition, the inherent weakness of the viral construct in the absence of suppressor adds an extra layer of environmental safety to the system.

The effect of removing the coat protein of TMV and portions of the movement protein has been examined. It was found that complete removal of the movement protein produced only small infection points, which could be rescued by the co-agroinoculation of p19 or of various sized portions of the TMV movement protein. Thus, an on/off effect similar to the one described here has been previously described. However, the effect was created with the removal of both the CP and MP genes, whereas here the MP of SHMV has been preserved. The MP gene is useful in agroinoculation in that it allows for viral movement and creates a stronger infection. If fewer cells than the optimal 100% support a viral infection, as is often true with tobamoviral infections compared to potexviral infections, the presence of the MP gene is useful.

SHEC has been shown herein to strongly infect a variety of legumes in the presence of silencing suppressor, a property lacking with any of the TMV vectors. Thus, SHEC could be used to test a candidate for correct protein folding and function in legumes before performing a long term project in the creation of transgenic legumes. SHEC would also be useful as an overexpression agroinoculation screen for an array of unknown genes. Its use as a VIGS vector would be precluded by the need for silencing suppressor coexpression. SHEC would be useful in an inducible transgenic system to replace 35S or other promoters. It has been shown in legumes that the SHEC induces much greater expression of GUS than a comparable 35S-driven nonviral vector.

The SHAC/GFP vector constructed demonstrated that a full length vector of SHMV could be constructed. This SHAC vector was unusual in that it moved more slowly through the plant than the TMV/GFP JL24, it caused almost no symptoms, and it was very stable in terms of retaining the GFP over long term passaging. In this respect, it might serve as a good VIGS vector, due to its low impact on the plant host. Many variations of SHAC could be made, such as using other tobamovirus CP genes, or simply replacing the subgenomic region without replacing the CP ORF, that would hopefully restore infectivity in legumes.

There are other three other viral vectors that are able to infect legumes. Clover yellow vein virus (Potyvirus group) was made into an expression vector with the viral transcript created by 35S. However, the plasmid DNA was introduced to the plant by biolistics rather than by agroinoculation. GFP fluorescence was imaged by UV microscopy in bean. Bean pod mottle virus is a comovirus which has been made into a vector which infects soybeans. It was shown to express GFP when viewed macroscopically, and its ability as a VIGS vector was demonstrated. Rather than agroinoculation, infection was achieved by in vitro transcription. Pea early browning virus (PEBV) is tobravirus which was developed into a VIGS vector for legumes. PEBV is able to enter the meristematic tissue and affect the development of the plant by silencing the gene corresponding to the foreign gene fragment expressed by the virus. The PEBV vector was used via agroinoculation.

Example 3 Plants

Nicotiana benthamiana was grown from seed and then transplanted and grown in 4″ plastic azalea pots in Sunshine Mix #1 under 400W metal halide lamps to 10-15 cm before inoculation. GFP fluorescence in whole plants was examined under long-wave UV light (UVL-56, UVProducts, Upland, Calif.) and photographs with a Canon Digital EOS Rebel XT camera (Canon Inc., Japan) equipped with a Hoya yellow (K2) filter (Hoya Corporation, Japan) was used.

General Methods

The high fidelity polymerase, Phusion (New England Biolabs (NEB), Beverly, Mass.), was used according to company protocols in all constructions. Recombinant clones were introduced into Escherichia coli NEB 10-beta electrocompetent cells by electroporation at 1.44 kV and 129Ω for 5 ms using a BTX 600 Electro Cell Manipulator (BTX Inc., San Diego, Calif., USA) and colonies were screened by PCR using NEB Taq polymerase or by restriction digests of plasmid minipreps prepared by Wizard Plus Miniprep Kit (Promega, Madison, Wis.).

Construction of JBest

The bialaphos resistance gene (bar) flanked by the promoter and terminator from the nopaline synthase gene of A. tumefaciens was transferred from the binary vector, pCB302, to the binary vector, JL22 (Lindbo, 2000a), via flanking HindIII and EcoRI sites to create pJL22/bar. Next, the 35S transcription start site of JL22, which allows an exact start of any virus blunt-end ligated into the StuI site (FIG. 3), was combined with the XVE/estradiol activated promoter of pER8 by overlap PCR. The pER promoter was amplified with primers EcoLexUp (SEQ ID NO:86) and 35termAS Down (SEQ ID NO:88) (FIG. 4) and the JL22 start site was amplified with 35StermUp and JL22RB Down; the two products were gel purified and then amplified for 5 cycles, after which the flanking EcoLexUp and JL22RB Down primers were used to complete the overlap PCR. The final product was inserted into JL22/bar at the EcoRI and PmeI (in RB) sites to create JBest (FIG. 3).

Construction of the TBest Series

An upstream phosphorylated PCR product of the 5′ 1027 nts of TMV was created using primers TMVp1-21Up (SEQ ID NO:90) and TMV1008NotDN(SEQ ID NO:91). This was inserted into the StuI blunt site and the NotI site of JBest. The various versions of TBest were created by inserting almost the entire TMV sequence from a previously made noninducible vector carried by the JL22 vector expressing a gene of interest. Specifically, the XmaI site at TMV nt256 and the PmeI site in the RB were used to transport the TMV sequence into JBest carrying the 5′ end of TMV to create each TBest vector (FIG. 3).

Construction of the FBest Series

As for the construction of the TBest series, an upstream phosphorylated PCR product of the 5′ 756 nts of FoMV was created using primers FoMV 5′ termUp (SEQ ID NO:92) and FoMV756NotIDown (SEQ ID NO:93). This was inserted into the StuI blunt site and the NotI site of JBest. The various versions of FBest were created as with TBest, but at different sites. Specifically, the PmlI site at FECT nt411 and the XbaI site at FECT nt4446 (after the poly(A) tail) were used to transport the FECT sequence into JBest carrying the 5′ end of FECT to create each FBest vector (FIG. 3).

The FBest vector (SEQ ID NO:42) comprises a T-DNA left border (SEQ ID NO:35), miscellaneous sequence (SEQ ID NO:36), a Nos promoter (SEQ ID NO:37), a bar gene (SEQ ID NO: 38), a Nos terminator (SEQ ID NO:39), a Lex operator (SEQ ID NO:40), and a 35S core promoter segment (SEQ ID NO:41).

Construction of pER8/p19

pER8/p19 was created by adding XhoI and SpeI sites to p19 by mutagenic PCR using primers p19XhoIUp (SEQ ID NO:94) and p19SpeIDown (SEQ ID NO:95). These sites were used for insertion of p19 into pER8 between the 35S promoter and pea3A terminator (FIG. 3).

Agroinoculation

Agroinfiltration was performed using standard procedures. Agrobacterium tumefaciens stain GV3101 was used for the agroinoculation of N. benthamiana. A. tumefaciens was transformed with plasmid constructs using the same conditions as for E. coli above. Agrobacterium transformants were selected at room temperature on Luria-Bertani plates containing 50 μg/ml kanamycin. A colony of A. tumefaciens was inoculated to 5 ml of L-MESA medium (LB media supplemented with 10 mM MES, 20 uM acetosyringone (Phytotechnology Labs, Shawnee Mission, Kans.), a wound response compound that elicits Agrobacterium virulence, and the same antibiotics), and grown overnight at room temperature. The cells of the overnight culture were harvested by centrifugation and resuspended in induction media (10 mM MES, 10 mM MgCl₂, 100 uM acetosyringone) for a final OD₆₀₀ of 1.0 and incubated for 2 h to overnight at room temperature. The cultures of A. tumefaciens were infiltrated into the underside of leaves of plants with a 3 ml syringe without needle. For agroinoculation of two or more bacterium cultures at the same time, multiple cultures of A. tumefaciens were mixed in equal amounts and infiltrated together.

Induction with Estradiol

Estradiol was prepared as a 10 mM stock in DMSO and diluted to 10 μM in deionized water. Plants were agroinoculated and then, 1-2 days later, the estradiol was administered by syringe injection or root drench (40 ml of 10 μM estradiol used to water one 4″ pot).

Results Induction of TBest

TBest carrying various genes of interest was inoculated onto N. benthamiana as a control experiment to determine the leakiness of the estradiol system when teamed with TMV, the most commonly used commercial vector of whole plants. Two days after inoculation, estradiol was applied to the plants either as a root drench or via syringe inoculation into the inoculated leaves. pER8/p19, expressing the silencing suppressor, p19, under the control of the estradiol inducible promoter, was co-inoculated in its own Agrobacterium culture along with an Agrobacterium culture containing an estradiol-inducible TBest construct (FIG. 3). TBest/GFP at four days post-estradiol (dpe) showed strong fluorescence in the inoculated zone in all plants, regardless of treatment: estradiol by syringe or by root drench or no estradiol at all. By 11 dpe, all of these plants also showed systemically moving fluorescence due to the mobility of the full length TMV vector.

To further test whether this system could be used to disrupt cell wall structures in order to produce plant material amenable to the production of bioethanol, two different cell wall modifying genes were transferred to TBest vectors. EngD, a cellulase from Clostridium cellulovorans, gave no necrosis when carried in the TBest vector, regardless of induction, even though it did produce some necrotic specks when expressed in the noninducible JL24 vector with constitutively expressed p19. On the other hand, lipid transfer protein (LTP-2 from tobacco) caused severe necrosis in all plants by 11 dpe, but the fastest development (1 to 4 dpe) was with either estradiol application. Thus, TBest suggested that difficulties with leakiness would make the use of full length TMV in an inducible form an unworkable approach.

Induction of FBest

FBest was used as a deleted virus vector alternative to TBest. FBest carrying either GFP or maize anther xylanase (mxyl) was inoculated to N. benthamiana plants along with estradiol inducible p19 carried in the pER8 binary vector and estradiol was applied by both syringe and root drench the next day. FBest/GFP, in the presence of induced p19, showed good fluorescence the day after estradiol induction, becoming very strong at 3 dpe, which is maintained afterwards. However, with no estradiol induction, very little fluorescence was detected at any time. FECT/GFP could substitute for FBest and achieve the same inducible on/off results in conjunction with inducible p19, with little or no fluorescence in the presence or absence of estradiol when p19 was absent or when 19 was present and estradiol was absent, but with strong fluorescence in the presence of estradiol and p19. No effects or symptoms, other than mechanical damage, were seen on pER8/p19/estradiol control plants. FBest/mxyl plants induced by estradiol showed confluent necrotic spots in the inoculated zones at 3 dpe but no symptoms at 1 dpe. Necrosis grew more severe by 6 dpe. In contrast, noninduced leaves showed scattered necrotic spots.

The necrosis obtained with EngD, LTP and mxyl cell wall-modifying enzymes was also observed with other enzymes expressed by the noninducible JL24. In order to determine whether this necrosis was due to a hypersensitive response to the pathogens involved (TMV and Agrobacterium) or to cell wall damage by the enzymes, N. bethamiana leaves were agroinoculated with various JL24/glycanase constructs and infiltrated with 0.5 M mannitol (allowing osmotic equilibrium between cytoplasm and surrounding medium) or water the next day. The inoculum consisted of 35S::p19 in a binary vector plus JL24 constructs expressing EngD, LTP-2, Jun a I (a pectinase) and XynA (a xylanase). After five days in their respective media, only the mannitol floated leaves were green. In contrast, inoculated leaves floated on water showed conspicuous necrosis in the inoculated zones.

In a control experiment, Nicotiana glutinosa, which is hypersensitive to TMV, was inoculated with TMV virions from the sap of an infected Nicotiana tabacum plant, a systemic host. The next day, the infected leaves were infiltrated and floated on 0.5 M mannitol or water. Both the mannitol and water treated leaves developed characteristic necrotic lesions.

Discussion

Inducible viral vector systems promise higher yields of target protein in replacing traditional inducible and noninducible promoters in agroinoculation (e.g., Sudarshana et al., 2006) and stable transgenic (e.g. Zhang and Mason, 2006) applications. UV macroscopic observations, both the FBest/GFP and the FECT/GFP) fluorescence with p19) had the fairly unique capacity to be not be washed out by indoor lighting and did not require darkness to be seen. FECT/GFP with p19 gave yields of GFP of 40% TSP, which is matched only by some recently developed TMV vectors (Lindo, 2007bGleba et al., 2005) and is 4-8-fold greater than the next more expressive viral vectors.

The leakiness of the TBest system was not seen in the FBest system. JL24, the noninducible TMV/GFP vector that TBest system is built upon, gives good fluorescence even without p19, while FECT, the noninducible version of FBest, yields very poor fluorescence. This concept of using an inducible version of a functionally crippled virus coupled with an inducible silencing suppressor to rescue the virus appears to be the reason for the low amount of leakiness with this system. Even a small amount of virus leaking into the cytoplasm will not be able to sustain a strong infection if only a small amount of silencing suppressor, insufficient to elicit silencing, is produced.

The use of a functionally crippled virus also enhances the environmental safety of this construct if used in agroinoculation or, as has been done for other published inducible viral vectors, if used as a stable transgenic expression cassette. FoMV is the parent virus of FBest and is noteworthy for its mild infections. FBest has 29% of its viral genome deleted and expresses GFP very poorly in the absence of a silencing suppressor. Thus, if carried as a cassette in a transgenic plant in the field, very little or no viral RNA would be available for translation to target protein or available for RNA recombination with wild viruses. The viral RNA would be expected to be noninfectious under normal situations, since it is unprotected by a virion coat. If infection did occur, however, the resulting infection would be expected to be fairly nonproductive in the presence of the silencing machinery of a normal plant.

One use for this system would be the production of target proteins, such as vaccines, that are toxic to plants. Liu and Kearney (unpublished data), for example, have expressed the allergen, Jun a 1, in tobacco by agroinoculation using a standard TMV vector. If this were to be used as a vaccine for large scale production in the field, a transgenic version would need to be produced. An inducible viral vector would be needed for this step since they allow for transgenic plants to be produced from tissue culture without the injury or silencing seen in noninducible vectors. FBest would allow for yields perhaps as high as presently possible in plants and would maintain an unusually high level of environmental safety during the process of field bulk up. The transgenic seed could be used to produce seedlings which could then be fed to livestock or poultry as an edible vaccine after induction.

Example 4 Plants

Nicotiana benthamiana was grown from seed and then transplanted and grown in 4″ plastic azalea pots in Sunshine Mix #1 under 400 W metal halide lamps to 10-15 cm before inoculation. GFP fluorescence in whole plants was examined under long-wave UV light (UVL-56, UVProducts, Upland, Calif.) and photographs with a Canon Digital EOS Rebel XT camera (Canon Inc., Japan) equipped with a Hoya yellow (K2) filter (Hoya Corporation, Japan) was used.

General Methods

The high fidelity polymerase, Phusion (New England Biolabs (NEB), Beverly, Mass.), was used according to company protocols in all constructions. Recombinant clones were introduced into Escherichia coli NEB 10-beta electrocompetent cells by electroporation at 1.44 kV and 129 n for 5 ms using a BTX 600 Electro Cell Manipulator (BTX Inc., San Diego, Calif., USA) and colonies were screened by PCR using NEB Taq polymerase or by restriction digests of plasmid minipreps prepared by Wizard Plus Miniprep Kit (Promega, Madison, Wis.).

Construction of JL22/WClMV

A clone was obtained from the New Zealand government agency, HortScience, and this construct contained the full length white clover mosaic virus (WClMV) (SEQ ID NO:20) sequence driven by a T7 RNA polymerase promoter in a standard E. coli cloning vector, and fully described by Beck et al. (1990). The WClMV comprises a 5′ UTR (SEQ ID NO: 14), a replicase ORF (SEQ ID NO:15), a TGB1 ORF (SEQ ID NO:16), TGB2 and TGB3 ORFs (SEQ ID NO:17), a CP ORF (SEQ ID NO:18), and a 3′ UTR (SEQ ID NO:19). Steps were then taken to transfer the sequence to a binary vector. First, two PCRs were performed to amplify the 5′ and 3′ sections of the virus. This is diagramed in FIG. 5, using primers listed in Table 2. The 5′ section was than cloned into binary vector, JL22, followed by the 3′ section. The remaining middle section of the viral sequence was retrieved from the original full length clone and inserted into the partial sequence in the binary vector using native restriction sites.

TABLE 3 Plasmids used in construction of the WECT vectors. SEQ ID Oligonucleotide Plasmid Primer (P) NO sequence (5′ → 3′) pJL22/WCIMV  1. WCIMV 5′ term UP 132  1. P-GAAAACAAGACGAGACGAACC (pWCIMV nt. 1-21)  2. WCIMV1089 NotI DN 133  2. AAAAAAGCGGCCGCGATAATCAGATAGCTCAGAA (pWCIMV nt. 1070-1089)  3. WCIMV4822 NotI UP 134  3. TATTATGCGGCCGCTTGGAGGTGAATACAAAGAC (pWCIMV nt. 4822-4841)  4. WCIMV5846 XbaI DN 135  4. AATGAATCTAGACTGAAATTTTATTAAACAGA (pWCIMV nt. 5846-5827) pWECT26atg  5. WCIMV2608XmaUP 136  5. AGAGTACCCGGGAGATCATCGCTGCTGAAGAA pWECT40atg (pWCIMV nt. 2599-2618)  6. WCIMVsg26PacDN 137  6. GAAGTCTTAATTAACTGAGGAGGTGGTGA (pWCIMV nt. 4020-4000)     ATGTGA  7. WCMVsg40PacDN 138  7. GAAGTCTTAATTAATAAAACCGTGGGAGC (pWCIMV nt. 4034-4014)     TGAGGA  8. WCMVPacI MluI 3'CP 139  8. AAGTTGTTAATTAA ACGCGT UP     GTTGAAATCACTAACGGTC  9. JL22RB DN 140  9. TCTAATAAACGCTCTTTTCTCTTAGGTT (pJL22 nt. 827-800) pWECT26atg/GFP 10. PacGFP UP 141 10. TTGTCATTAATTAAGCTAGCAAAGGAGAAGAAC pWECT40atg/GFP 11. GFP Bss DN 142 11. TTTACTGCGCGCTTATTTGTAGAGCTCATCCA 12. WCMV2590 XmaI UP 143 12. TGCGTACCCGGGAAATGAATGAGATCATCGCTGC (pWCIMV nt. 2590-2611) pWECT25 13. WECT + 22ORF 144 13. GTACTATTAATTAA pWECT40 PacDN     GGAGGTGGTGAATGTGATCGATCGCTACT (pWCIMV nt. 4016-3988) 14. WECT + 40ORF 145 14. GACTACTTAATTAA PacDN     AACCGTGGGAGCTGAGGAGGTGGTGAATGTGAT (pWCIMV nt. 4031-3999) pWECT25[2] 15. WECT UPscreen 146 15. GAATGAGATCATCGCTGC pWECT40[2] (pWCIMV nt. 2594-2611) 16. WECTscreen AUC 147 16. AGGTGGTGAATGTGATCG (pWCIMV nt. 3997-4014) 17. WECT40screen 148 17. TAAAACCGTGGGAGCTGA (pWCIMV nt. 4017-4034)

Construction of WECTatg

The TGB and CP genes were wholly or partially removed by two PCRs of the viral sections flanking the deletion site (FIG. 6). Primers binding to either side of the deletion site were created which also contained PacI and MluI sites that would constitute the multiple cloning site of WECT. The PCR product of the 3′ viral sequence was placed into the cloning vector, pNEB193, and then the 5′ viral sequence was placed upstream of it in the same vector. This combined sequence, which lacks the TGB2 and TGB3 genes and most of the TGB1 and CP genes, was placed back into the JL22/WClMV clone via native WClMV Xba I sites. Differing amounts of TGB1 ORF sequence were removed to determine how much of this sequence had a role as part of the subgenomic promoter. Two different length were created using primers P6 and P7 (FIG. 6). In a preferred embodiment, approximately 30% or less of the initial sequence of the TGB1 ORF would be retained, preferably approximately 20% or less of the initial sequence of the TGB1 ORF would be retained, most preferably approximately 6% or less of the initial sequence of the TGB2 ORF comprising the initial 40 by of the 688 by sequence would be retained. In a preferred embodiment, approximately 30% or less of the final sequence of the CP ORF would be retained, preferably approximately 20% or less of the final sequence of the CP ORF would be retained, most preferably approximately 10% or less of the final sequence of the TGB2 ORF comprising the final 60 by of the 627 by sequence would be retained.

Construction of WECT

In order to change the TGB1 start codon to ATC, a mutagenic primer (P13) was used in a PCR (FIG. 7). This PCR product was inserted back into WECTatg to create WECT25. The middle section of WECT40, which has a longer subgenomic promoter (40 bases of TGB1 ORF rather than 25 bases), was created by PCR with primer P14 using WECT25 as a template. WECT40 was created by inserting this PCR product into WECT40atg using the Ahd I and Pac I sites.

WECT40 vector (SEQ ID NO:85) comprises a 5′ UTR (SEQ ID NO:73), a replicase ORF (SEQ ID NO:74), 40 by of TGB1 ORF (SEQ ID NO:75), PacI and MluI cloning sites followed by the last 60 by of CP ORF (SEQ ID NO:76), a 3′ UTR (SEQ ID NO:77), a 35S terminator (SEQ ID NO:78), miscellaneous sequence (SEQ ID NO:79), a T-DNA right border (SEQ ID NO:80), a JL22 sequence (SEQ ID NO:81), a T-DNA left border (SEQ ID NO:82), miscellaneous sequence 2 (SEQ ID NO:83), and a 35S promoter (SEQ ID NO:84).

Agroinoculation

Agroinfiltration was performed as described (Kapila et al., 1997) with modifications. Agrobacterium tumefaciens stain GV3101 was used for the agroinoculation of N. benthamiana. A. tumefaciens was transformed with plasmid constructs using the same conditions as for E. coli above. Agrobacterium transformants were selected at room temperature on Luria-Bertani plates containing 50 μg/ml kanamycin. A colony of A. tumefaciens was inoculated to 5 ml of L-MESA medium (LB media supplemented with 10 mM MES, 20 uM acetosyringone (Phytotechnology Labs, Shawnee Mission, Kans.), a wound response compound that elicits Agrobacterium virulence, and the same antibiotics), and grown overnight at room temperature. The cells of the overnight culture were harvested by centrifugation and resuspended in induction media (10 mM MES, 10 mM MgCl₂, 100 uM acetosyringone) for a final OD₆₀₀ of 1.0 and incubated for 2 h to overnight at room temperature. The cultures of A. tumefaciens were infiltrated into the underside of leaves of plants with a 3 ml syringe without needle. For agroinoculation of two or more bacterium cultures at the same time, multiple cultures of A. tumefaciens were mixed in equal amounts and infiltrated together.

Results

Expression of GFP by WECT in Nicotiana benthamiana

The subgenomic promoter length affected the expression of GFP in WECT. WECT25/GFP expressed GFP less well than FECT40/GFP but WECT40/GFP was indistinguishable from FECT40/GFP. When plants were agroinoculated and infection was allowed to proceed for four days, WECT25/GFP agroinoculated plants were seen by UV light to have moderate fluorescence in the inoculated zones, whereas plants agroinoculated with WECT40/GFF' or FECT40/GFP had very strongly fluorescent zones. Similar to FECT40, there was little of no expression of GFP in the absence of the p19 silencing suppressor.

Expression of GFP by WECT in Legumes

Expression of GFP by WECT40/GFP in legumes was not robust as in N. benthamiana. However, infection was readily seen in pea and especially in chickpea and lentil as multitudes of clearly fluorescent cells under UV fluorescence microscopy. In contrast, few or no fluorescent cells were seen in uninoculated controls of these plants.

Discussion

The performance of the WECT vectors remarkably paralleled that of the FECT vectors. The optimal size of the TGB1 subgenomic promoter for driving GFP expression was found to include at least 40 bases or TGB1 ORF for both WECT and FECT. There was little or no expression of GFP from the WECT vectors in the absence of p19 silencing suppressor. In side by side comparison, the GFP expression level appeared to be equivalent, by eye, to that of FECT, though SDS-PAGE analysis of actual protein levels has not yet been conducted. It is also notable that WECT infected legume species that FECT infected poorly or not at all, namely, chickpea and pea, as well as infecting lentil well, which FECT also infected.

Perhaps most interesting is the contrast between FECT and WECT vectors to a vector constructed from another potexvirus, PVX. Komarova et al. (2006), removed the TGB2 and TGB3 genes plus most of the TGB1 ORF, leaving only the first 5% of the TGB1 ORF (thought to be functionally a part of the TGB1 subgenomic promoter and needed to drive foreign gene expression). In the PVX vector, the entire CP ORF was removed, but, since this gave no GFP expression in the FECT vector, the final 42 bases of CP ORF were included in the WECT construction, just as was done for FECT. Though the PVX vector was nearly identical, it was quite a capable vector in the absence of p19. This is in complete contrast to the FECT and WECT vectors, which are almost entirely dependent on p19 for any foreign gene expression.

It is reasonable to conclude, then, that some potexviruses can be made into vectors with the silencing supressor-dependent “on/off” switch herein described, and others cannot. The value of this switch is two-fold. First, the virus is essentially crippled in a plant with a normal RNA silencing system. Even if the virus were to survive in the environment and infect a plant (which would be unlikely due to the lack of a CP gene), the infection would be nonproductive. Only when the silencing suppressor is supplied does the virus replicate significantly. Second, an inducible system should be able to be made, similar to that of the FECT vector, in which viral replication is dependent on the presence of high p19 levels and therefore “nonleaky” when not induced. In contrast, other “noncrippled” viruses need only have one viral RNA exported to the cytoplasm for to process towards full viral replication levels to commence.

REFERENCES CITED

The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

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1. A viral vector system comprising: 1) a viral vector carried on a binary vector, wherein the viral vector is expressed via a viral vector promoter, with expression terminating via a viral vector polyA signal/transcription terminator at the 3′ end of the viral vector, and the viral vector comprises a deleted foxtail mosaic virus (FoMV) full length cDNA; wherein the deleted FoMV full length cDNA is a modified wildtype FoMV full length cDNA such that the TGB2 and TGB3 genes are deleted, all bases except the beginning of the TGB1 gene are deleted, all bases except the 3′ end of the CP gene are deleted, the subgenomic promoter of subgenomic RNA1 is retained, and the start codon of the TGB1 open reading frame has been mutated to be non-functional; wherein the beginning of the TGB1 open reading frame is 30% or less of the initial sequence of the open reading frame of TGB1; and wherein the 3′ end of the CP gene is 30% or less of the terminal sequence of the CP FoMV gene; and 2) a second binary vector carrying a gene for a silencing suppressor, driven by a silencing suppressor promoter.
 2. The viral vector system of claim 1, wherein a heterologous gene has been inserted into restriction sites at the 3′ end of the subgenomic promoter of subgenomic RNA1.
 3. The viral vector system of claim 1, wherein the silencing suppressor is p19 or HcPro, and the silencing suppressor promoter is 35S.
 4. The viral vector system of claim 1, wherein the viral vector promoter is an XVE/estradiol activated promoter of pER8 or a constitutive promoter, and the second binary vector comprises an XVE transcription factor gene and the silencing suppressor promoter is an XVE/estradiol activated promoter.
 5. A process for expressing genes in a plant, comprising: agroinoculating the plant with the viral vector system of claim
 1. 6. The process of claim 5, wherein the plant is Nicotiana benthamiana, lentil, Medicagol trunculata, barley, wheat or switchgrass.
 7. The process of claim 5, wherein the plant is classified in the taxonomic family of Fabaceae or Poaceae.
 8. A process for expressing genes in a plant, comprising: agroinoculating the plant with the viral vector system of claim 4 with the two binary vectors each in a separate Agrobacterium line.
 9. The process of claim 8, further comprising induction of the XVE/estradiol activated promoter with estradiol.
 10. The process of claim 9, wherein the induction is carried out by either root drench or syringe injection of estradiol.
 11. A viral vector system comprising: 1) a binary vector containing a viral vector, wherein the viral vector is expressed via a viral vector promoter, with expression terminating via a viral vector polyA signal/transcription terminator at the 3′ end of the viral vector, and the viral vector comprises a deleted sunn hemp mosaic virus (SHMV) full length cDNA, wherein the deleted SHMV full length cDNA is a modified wildtype SHMV full length cDNA such that all bases except the 5′ end of the CP gene are deleted, and wherein the start codon of the CP open reading frame has been mutated to be non-functional; and wherein the 5′ end of the CP gene is the terminal 20% or less of the 5′ end of the CP ORF sequence; and 2) a second binary vector carrying a gene for a silencing suppressor, driven by a silencing suppressor promoter.
 12. The viral vector of claim 11, wherein a heterologous gene has been inserted into the sites where the CP gene was deleted.
 13. The viral vector system of claim 11, wherein the silencing suppressor is p19 or HcPro, and the silencing suppressor promoter is 35S.
 14. The viral vector system of claim 11, wherein the viral vector promoter is an XVE/estradiol activated promoter of pER8 or a constitutive promoter, and the second binary vector comprises an XVE transcription factor gene and the silencing suppressor promoter is an XVE/estradiol activated promoter.
 15. A process for expressing genes in a plant, comprising: agroinoculating the plant with the binary vector of claim
 11. 16. The process of claim 18, wherein the plant is Nicotiana benthamiana, bean, Medicago trunculata, or cowpea.
 17. A process for expressing genes in a plant, comprising: agroinoculating the plant with the viral vector system of claim
 14. 18. The process of claim 17, further comprising induction of the XVE/estradiol activated promoter with estradiol.
 19. The process of claim 18, wherein the induction is carried out by either root drench or syringe injection of estradiol.
 20. A viral vector system comprising: 1) a viral vector carried on a binary vector, wherein, the viral vector is expressed via a viral vector promoter system, with expression terminating via a viral vector polyA signal/transcription terminator at the 3′ end, and the viral vector comprises a deleted white clover mosaic virus (WClMV) sequence full length cDNA; wherein the deleted WClMV sequence full length cDNA is a modified wildtype WClMV full length cDNA such that the TGB2 and TGB3 genes are deleted, all bases except the initial portion of the TGB1 gene are deleted, all bases except the 3′ end of the CP gene are deleted, the subgenomic promoter of subgenomic TGB1 RNA is retained, and the start codon of the TGB1 open reading frame has been mutated to be non-functional; wherein the beginning of the TGB1 open reading frame is the initial 30% or less of the open reading frame of TGB1; and wherein the 3′ end of the CP gene is the terminal 30% or less of the 3′ terminal sequence of the CP WClMV gene; and 2) a second binary vector carrying a gene for a silencing suppressor, driven by a silencing suppressor promoter.
 21. The viral vector of claim 20, wherein a heterologous gene has been inserted into restriction sites at the 3′ end of the subgenomic promoter of subgenomic TGB1 RNA.
 22. The viral vector system of claim 20, wherein the silencing suppressor is p19 or HcPro, and the silencing suppressor promoter is 35S.
 23. The viral vector system of claim 20, wherein the viral vector promoter is an XVE/estradiol activated promoter of pER8 or a constitutive promoter, and the second binary vector comprises an XVE transcription factor gene and the silencing suppressor promoter is an XVE/estradiol activated promoter.
 23. A process for expressing genes in a plant, comprising: agroinoculating the plant with the viral vector of claim
 20. 24. The process of claim 23, wherein the plant is Nicotiana benthamiana, chickpea, lentil, or pea.
 25. A process for expressing genes in a plant, comprising: agroinoculating the plant with the viral vector system of claim
 23. 26. The process of claim 25, further comprising induction of the XVE/estradiol activated promoter with estradiol.
 27. The process of claim 26, wherein the induction is carried out by either root drench or syringe injection of estradiol.
 28. A method of expressing a gene in a plant comprising the steps of: (a) delivering a viral vector to the plant; wherein the viral vector is carried by a viral binary vector and the viral vector is expressed via a viral vector promoter, with expression terminating via a viral vector polyA signal/transcription terminator at the 3′ end of the viral vector, and the viral vector comprises a deleted foxtail mosaic virus (FoMV) full length cDNA; wherein the deleted FoMV full length cDNA is a modified wildtype FoMV full length cDNA such that the TGB2 and TGB3 genes are deleted, all bases except the beginning of the TGB1 gene are deleted, all bases except the 3′ end of the CP gene are deleted, the subgenomic promoter of subgenomic RNA1 is retained, and the start codon of the TGB1 open reading frame has been mutated to be non-functional; wherein the beginning of the TGB1 open reading frame is 30% or less of the initial sequence of the open reading frame of TGB1; and wherein the 3′ end of the CP gene is 30% or less of the terminal sequence of the CP FoMV gene (b) a silencing suppressor wherein the silencing suppressor is delivered via a silencing suppressor vector comprising a silencing suppressor open reading frame, and wherein the expression of the silencing suppressor open reading frame is driven by a silencing suppressor promoter and terminated by a silencing suppressor polyA signal transcription terminator; wherein the viral vector may be constitutively or inducibly expressed; and wherein the silencing suppressor vector may be constitutively or inducibly expressed.
 29. A method of expressing a gene in a plant comprising the steps of: (a) delivering a viral vector to the plant; wherein the viral vector is carried by a viral binary vector and the viral vector is expressed via a viral vector promoter, with expression terminating via a viral vector polyA signal/transcription terminator at the 3′ end of the viral vector, and the viral vector comprises a deleted sunn hemp mosaic virus (SHMV) full length cDNA, wherein the deleted SHMV full length cDNA is a modified wildtype SHMV full length cDNA such that all bases except the 5′ end of the CP gene are deleted, and wherein the start codon of the CP open reading frame has been mutated to be non-functional; wherein the 5′ end of the CP gene is the terminal 20% or less of the 5′ end of the CP ORF sequence; and (b) a silencing suppressor wherein the silencing suppressor is delivered via a silencing suppressor vector comprising a silencing suppressor open reading frame, and wherein the expression of the silencing suppressor open reading frame is driven by a silencing suppressor promoter and terminated by a silencing suppressor polyA signal/transcription terminator; wherein the viral vector may be constitutively or inducibly expressed; and wherein the silencing suppressor vector may be constitutively or inducibly expressed.
 30. A method of expressing a gene in a plant comprising the steps of: (a) delivering a viral vector to the plant; wherein the viral vector is carried by a viral binary vector and the viral vector is expressed via a viral vector promoter system, with expression terminating via a viral vector polyA signal/transcription terminator at the 3′ end, and the viral vector comprises a deleted WClMV sequence full length cDNA; wherein the deleted WClMV sequence full length cDNA is a modified wildtype WClMV full length cDNA such that the TGB2 and TGB3 genes are deleted, all bases except the initial portion of the TGB1 gene are deleted, all bases except the 3′ end of the CP gene are deleted, the subgenomic promoter of subgenomic RNA1 is retained, and the start codon of the TGB1 open reading frame has been mutated to be non-functional; wherein the beginning of the TGB1 open reading frame is the initial 30% or less of the open reading frame of TGB1; and wherein the 3′ end of the CP gene is the terminal 30% or less of the 3′ terminal sequence of the CP WClMV gene; and (b) a silencing suppressor wherein the silencing suppressor is delivered via a silencing suppressor vector containing a silencing suppressor open reading frame, and wherein the expression of the silencing suppressor open reading frame is driven by an inducible silencing suppressor promoter system and terminated by a silencing suppressor polyA signal/transcription terminator; wherein the viral vector may be constitutively or inducibly expressed; and wherein the silencing suppressor vector may be constitutively or inducibly expressed. 